Pmst1 mutants for chemoenzymatic synthesis of sialyl lewis x compounds

ABSTRACT

The present invention provides mutants of PmST1 for the preparation of sialyl-Lewis x  oligosaccharides, and other sialosides with decreased sialidase activity.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a continuation application of the U.S. applicationSer. No. 14/237,334 filed Jun. 18, 2014, now U.S. Pat. No. 9,255,257,the National Stage Entry of PCT Application No. PCT/US2012/049748, filedAug. 6, 2012, which claims priority to U.S. Provisional Application No.61/515,702, filed Aug. 5, 2011 which is incorporated in its entiretyherein for all purposes.

STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSOREDRESEARCH AND DEVELOPMENT

This invention was made with Government support under Grant Nos.R01HD065122 awarded by National Institutes of Health. The Government hascertain rights in this invention.

BACKGROUND OF THE INVENTION

Glycosyltransferase-catalyzed reactions have gained increasing attentionand application for the synthesis of complex carbohydrates andglycoconjugates. Most mammalian glycosyltransferases suffer from no orlow expression in E. coli systems and more restricted substratespecificity. In comparison, bacterial glycosyltransferases are generallyeasier to access using E. coli expression systems and have morepromiscuous substrate flexibility. Nevertheless, despite the discoveryof many bacterial glycosyltransferases which have promiscuities for bothdonor and acceptor substrates, the application of glycosyltransferasesin the synthesis of carbohydrate-containing structures is limited by theavailability and the substrate specificity of wild-type enzymes.

For example, sialyltransferases, the key enzymes that catalyze thetransfer of a sialic acid residue from cytidine 5′-monophosphate-sialicacid (CMP-sialic acid) to an acceptor, have been commonly used for thesynthesis of sialic acid-containing structures. Sialyl Lewis^(x)[SLe^(x), Siaα2-3Galβ1-4(Fucα1-3)GlcNAcαOR] is an important carbohydrateepitope involved in inflammation as well as adhesion and metastasis ofcancer cells. It is a well-known tumor-associated carbohydrate antigenand has been used as a candidate for cancer vaccine. The biosynthesis ofSLe^(x) involves the formation of Siaα2-3Galβ1-4GlcNAcαOR catalyzed byan α2-3-sialyltransferase followed by anα1-3-fucosyltransferase-catalyzed fucosylation. This biosyntheticsequence usually cannot be altered as common α2-3-sialyltransferases donot use fucose-containing Lewis^(x) [Le^(x), Galβ1-4(Fucα1-3)GlcNAcαOR]as a substrate.

As common terminal monosaccharides, sialic acids constitute a family ofgreat structural diversity. So far, more than 50 structurally distinctsialic acid forms have been identified in nature. To obtain SLe^(x) withdifferent sialic acid forms to elucidate the biological significance ofnaturally occurring sialic acid modifications, an efficient enzymaticapproach is to use Le^(x) [Galβ1-4(Fucα1-3)GlcNAcαOR] as afucose-containing acceptor to add different sialic acid forms by asuitable α2-3-sialyltransferase. This process of introducing differentforms of sialic acid onto the common fucosylated acceptor Le^(x) in thelast step has significant advantages compared to the normal SLe^(x)biosynthetic pathway in which fucosylation is the last glycosylationprocess. It not only simplifies the synthetic scheme as a less number ofreactions are needed, but also makes the purification process mucheasier as negatively charged SLe^(x) product is separated from neutralLe^(x) oligosaccharide instead of separating both negatively chargedoligosaccharides SLe^(x) and non-fucosylated sialosides if fucosylationoccurs in the last step.

We and others have demonstrated that a myxoma virusα2-3-sialyltransferase can use Le^(x) as an acceptor substrate forsynthesizing SLe^(x). Nevertheless, the low expression level of theenzyme in E. coli (<0.1 mg L⁻¹ culture) limits its application inpreparative and large-scale synthesis of SLe^(x).

We have previously shown that a multifunctional α2-3-sialyltransferasefrom Pasteurella multocida (PmST1) has a good expression level in E.coli (100 mg L⁻¹ culture) (J. Am. Chem. Soc. 2005, 127, 17618-17619.).It can use Le^(x) as an acceptor for the synthesis of SLe^(x) but theyields are poor (<20%) in spite of different conditions tested. What isneeded, therefore, are α2-3-sialyltransferases having goodα2-3-sialyltransferase activity with good expression levels, and loweredα2-3-sialidase or donor substrate hydrolysis activity. Surprisingly, thepresent invention meets this and other needs.

BRIEF SUMMARY OF THE INVENTION

In some embodiments, the present invention provides an isolatedglycosyltransferase, wherein the amino acid of the glycosyltransferasecorresponding to position 120 of SEQ ID NO:1 is any amino acid otherthan M, the amino acid the glycosyltransferase corresponding to position247 of SEQ ID NO:1 is any amino acid other than E, or the amino acid theglycosyltransferase corresponding to position 289 of SEQ ID NO:1 is anyamino acid other than R. The glycosyltransferase of the presentinvention has decreased α2-3 sialidase or donor substrate hydrolysisactivity compared to a control glycosyltransferase, wherein the aminoacid of the control glycosyltransferase corresponding to position 120 ofSEQ ID NO:1 is M, the amino acid of the control glycosyltransferasecorresponding to position 247 of SEQ ID NO:1 is E, and the amino acid ofthe control glycosyltransferase corresponding to position 289 of SEQ IDNO:1 is R. Finally, the glycosyltransferase of the present invention canbe a member of the glycosyltransferase family 80 (GT80).

In some embodiments, the present invention provides a recombinantnucleic acid encoding an isolated glycosyltransferase of the presentinvention.

In some embodiments, the present invention provides a cell including arecombinant nucleic acid of the present invention.

In some embodiments, the present invention provide a method of preparingan oligosaccharide, the method including forming a reaction mixtureincluding an acceptor sugar, a donor substrate of a sugar moiety and anucleotide, and the glycosyltransferase of the present invention, underconditions sufficient to transfer the sugar moiety from the donorsubstrate to the acceptor sugar, thereby forming the oligosaccharide.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A-1B show the ternary crystal structure of PmST1 (PDB ID: 21HZ)with bound CMP-3F(axial)-Neu5Ac and lactose (Figure A) and the structureof the modeled PmST1 double mutant E271F/R313Y of PmST1 wild typesequence SEQ ID NO: 13 (Figure B). The mutation sites are underlined.The mutant structure was obtained from automated homology modeling usingSwiss-Model.

FIG. 2 shows acceptor substrate specificity data for theα2-3-sialyltransferase activity of wild-type PmST1 (white columns) andits double mutant E271F/R313Y of PmST1 wild type sequence SEQ ID No: 13(black columns).

FIG. 3 shows thermal stability data for the α2-3-sialyltransferaseactivity of wild-type PmST1 (white columns) and its double mutantE271F/R313Y of PmST1 wild type sequence SEQ ID No: 13 (black columns).

FIG. 4 shows HPLC-based time course studies of PmST1-catalyzedα2-3-sialylation of Lewis^(x) trisaccharide (1 mM) with periodicaladdition of sialyltransferase donor CMP-Neu5Ac (indicated by arrows).Numbers in parentheses represent the % consumption of CMP-Neu5Ac bycapillary electrophoresis (CE) assays.

FIG. 5 illustrates that water (in the donor hydrolysis reaction)competes with Lewis' (in PmST1-catalyzed α2-3-sialylation reaction) forthe consumption of CMP-Neu5Ac.

FIG. 6 shows the SDS-PAGE analysis of the M144D mutant of PmST1 wildtype sequence SEQ ID No: 13. Lane 1: Protein marker; Lane 2: Whole cellsbefore induction; Lane 3: Whole cells after induction; Lane 4: Celllysate; Lane 5: Purified fraction.

FIG. 7A-7C—show the structural comparison between wild-type (WT) PmST1and M144D mutant of PmST1 wild type sequence SEQ ID No: 13 with boundCMP. FIG. 7A shows the overall structure alignment of WT PmST1 and thePmST1 M144D mutant, both with CMP bound. FIG. 7B shows the stereo viewof the superposition near the active site for WT PmST1 and the M144Dmutant with bound CMP-3F(a)-Neu5Ac (a donor substrate analog) andlactose acceptor. FIG. 7C shows the active site of the ternary crystalstructure of PmST1 (PDB 1D: 21HZ) with bound CMP-3F(axial)-Neu5Ac andlactose.

FIG. 8 shows ¹⁵N-¹H HSQC NMR spectra of ¹⁵N-labeled PmST1 (WT versusM144D mutant of PmST1 wild type sequence SEQ ID NO: 13; as well as apoversus CMP-bound).

FIG. 9 shows the one-pot three-enzyme synthesis of sialyl Le^(x)βProN₃(SLe^(x)βProN₃) containing different forms of sialic acids fromLe^(x)βProN₃. Aldolase refers to Pasteurella multocida sialic acidaldolase, and NmCSS refers to Neisseria meningitidis CMP-sialic acidsynthetase.

FIG. 10 shows amino acid sequences alignment of GT80 sialyltransferases.Pp_Pst3-1 (GenBank accession number BAF63530), Psp_Pst3-2 (GenBankaccession number BAF92025), Vsp_2,3ST (GenBank accession numberBAF91160), P1ST6_JT-1 (GenBank accession number BAF91416), P1ST6_JT-2,(GenBank accession number BAI49484), Pd2,6ST (GenBank accession numberBAA25316), Psp_pst6-1 (GenBank accession number BAF92026), Pm0188Ph(GenBank accession number DQ087233), and Hd0053P (GenBank accessionnumber AAP95068).

DETAILED DESCRIPTION OF THE INVENTION I. General

The present invention provides alpha2-3 sialyltransferase mutants ofPmST1 having reduced alpha2-3 sialidase or donor substrate hydrolysis,useful for the preparation of oligosaccharides, and can be tolerant offucosylated oligosaccharides. The mutations described herein can beincorporated into a variety of sialyltransferases to produce mutantshaving reduced sialidase or donor substrate activity.

II. Definitions

As used herein, the term “glycosyltransferase” refers to a polypeptidethat catalyzes the formation of a glycoside or an oligosaccharide from adonor substrate and an acceptor or acceptor sugar. In general, aglycosyltransferase catalyzes the transfer of the monosaccharide moietyof the donor substrate to a hydroxyl group of the acceptor. The covalentlinkage between the monosaccharide and the acceptor sugar can be a 1-4linkage, a 1-3 linkage, a 1-6-linkage, a 1-2 linkage, a 2-3-linkage, a2-6-linkage, a 2-8-linkage, or a 2-9-linkage. The linkage may be in theα- or β-configuration with respect to the anomeric carbon of themonosaccharide. Other types of linkages may be formed by theglycosyltransferases in the methods of the invention.Glycosyltransferases include, but are not limited to,sialyltransferases, heparosan synthases (HSs), glucosaminyltransferases,N-acetylglucosaminyltransferases, glucosyltransferases,glucuronyltransferases, N-acetylgalactosaminyltransferases,galactosyltransferases, galacturonyltransferases, fucosyltransferases,mannosyltransferases, xylosyltransferases. Sialyltransferases areenzymes that catalyze the transfer of sialic acid, or analogs thereof,to a monosaccharide or an oligosaccharide. In some embodiments, theglycosyltransferases useful in the present invention include those inGlycosyltransferase family 80 (GT80 using CAZy nomenclature), andincludes beta-galactoside alpha-2,3-sialyltransferases that catalyze thefollowing conversion: CMP-sialic acid+β-D-galactosyl-R=CMP+α-sialicacid-(2→3)-β-D-galactosyl-R, where the acceptor is GalβOR, where R is H,a monosaccharide, an oligosaccharide, a polysaccharide, a glycopeptide,a glycoprotein, or a glycolipid. GT80 family sialyltransferases alsoinclude galactoside or N-acetylgalactosaminidealpha-2,6-sialyltransferases that catalyze the following conversion:CMP-sialic acid+galactosyl/GalNAc-R=CMP+α-sialicacid-(2→3)-β-D-galactosyl/GalNAc-R, where the acceptor is GalOR orGalNAcOR, where R is H, serine or threonine on a peptide or protein, amonosaccharide, an oligosaccharide, a polysaccharide, a glycopeptide, aglycoprotein, or a glycolipid.

“Alpha2-3-sialidase” refers to an enzyme that catalyzes the hydrolysisof alpha2-3-glycosidic linkages of terminal sialic acids onoligosaccharides.

“Donor substrate hydrolysis” refers to hydrolysis of thenucleotide-sugar bond of the donor substrate.

An “amino acid” refers to any monomer unit that can be incorporated intoa peptide, polypeptide, or protein. As used herein, the term “aminoacid” includes the following twenty natural or genetically encodedalpha-amino acids: alanine (Ala or A), arginine (Arg or R), asparagine(Asn or N), aspartic acid (Asp or D), cysteine (Cys or C), glutamine(Gln or Q), glutamic acid (Glu or E), glycine (Gly or G), histidine (Hisor H), isoleucine (Ile or I), leucine (Leu or L), lysine (Lys or K),methionine (Met or M), phenylalanine (Phe or F), proline (Pro or P),serine (Ser or S), threonine (Thr or T), tryptophan (Trp or W), tyrosine(Tyr or Y), and valine (Val or V). In cases where “X” residues areundefined, these should be defined as “any amino acid.” The structuresof these twenty natural amino acids are shown in, e.g., Stryer et al.,Biochemistry, 5^(th) ed., Freeman and Company (2002), which isincorporated by reference. Additional amino acids, such asselenocysteine and pyrrolysine, can also be genetically coded for(Stadtman (1996) “Selenocysteine,” Annu Rev Biochem. 65:83-100 and Ibbaet al. (2002) “Genetic code: introducing pyrrolysine,” Curr Biol.12(13):R464-R466, which are both incorporated by reference). The term“amino acid” also includes unnatural amino acids, modified amino acids(e.g., having modified side chains and/or backbones), and amino acidanalogs.

“Polypeptide,” “peptide,” and “protein” are used interchangeably hereinto refer to a polymer of amino acid residues. All three terms apply toamino acid polymers in which one or more amino acid residue is anartificial chemical mimetic of a corresponding naturally occurring aminoacid, as well as to naturally occurring amino acid polymers andnon-naturally occurring amino acid polymers. As used herein, the termsencompass amino acid chains of any length, including full-lengthproteins, wherein the amino acid residues are linked by covalent peptidebonds.

The term “mutant,” in the context of glycosyltransferases of the presentinvention, means a polypeptide, typically recombinant, that comprisesone or more amino acid substitutions relative to a corresponding,naturally-occurring or unmodified glycosyltransferase, such as analpha2-3 sialyltransferase.

In the context of glycosyltransferases, “corresponding to” anothersequence (e.g., regions, fragments, nucleotide or amino acid positions,or the like) is based on the convention of numbering according tonucleotide or amino acid position number and then aligning the sequencesin a manner that maximizes the percentage of sequence identity. Becausenot all positions within a given “corresponding region” need beidentical, non-matching positions within a corresponding region may beregarded as “corresponding positions.” Accordingly, as used herein,referral to an “amino acid of the glycosyltransferase corresponding toposition [X]” of a specified glycosyltransferase refers to equivalentpositions, based on alignment, in other glycosyltransferases andstructural homologues and families. In some embodiments of the presentinvention, “correspondence” of amino acid positions are determined withrespect to a region of the glycosyltransferase comprising one or moremotifs of SEQ ID NO:1, 13, 15, 17, 19, 21, 23, 25, 27 or 29. When aglycosyltransferase polypeptide sequence differs from SEQ ID NO:1, 13,15, 17, 19, 21, 23, 25, 27 or 29 (e.g., by changes in amino acids oraddition or deletion of amino acids), it may be that a particularmutation associated with improved activity as discussed herein will notbe in the same position number as it is in SEQ ID NO:1, 13, 15, 17, 19,21, 23, 25, 27 or 29.

A nucleic acid is “operably linked” when it is placed into a functionalrelationship with another nucleic acid sequence. For example, a promoteror enhancer is operably linked to a coding sequence if it affects thetranscription of the sequence; or a ribosome binding site is operablylinked to a coding sequence if it is positioned so as to facilitatetranslation.

As used herein, “percent sequence identity” is determined by comparingtwo optimally aligned sequences over a comparison window, wherein theportion of the sequence in the comparison window can comprise additionsor deletions (i.e., gaps) as compared to the reference sequence (whichdoes not comprise additions or deletions) for optimal alignment of thetwo sequences. The percentage is calculated by determining the number ofpositions at which the identical nucleic acid base or amino acid residueoccurs in both sequences to yield the number of matched positions,dividing the number of matched positions by the total number ofpositions in the window of comparison and multiplying the result by 100to yield the percentage of sequence identity.

The terms “identical” or “identity,” in the context of two or morenucleic acids or polypeptide sequences, refer to two or more sequencesor subsequences that are the same. Sequences are “substantiallyidentical” to each other if they have a specified percentage ofnucleotides or amino acid residues that are the same (e.g., at least20%, at least 25%, at least 30%, at least 35%, at least 40%, at least45%, at least 50%, at least 55%, at least 60%, at least 65%, at least70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least95% identity over a specified region), when compared and aligned formaximum correspondence over a comparison window, or designated region asmeasured using one of the following sequence comparison algorithms or bymanual alignment and visual inspection. These definitions also refer tothe complement of a test sequence. Optionally, the identity exists overa region that is at least about 50 nucleotides in length, or moretypically over a region that is 100 to 500 or 1000 or more nucleotidesin length.

The terms “similarity” or “percent similarity,” in the context of two ormore polypeptide sequences, refer to two or more sequences orsubsequences that have a specified percentage of amino acid residuesthat are either the same or similar as defined by a conservative aminoacid substitutions (e.g., 60% similarity, optionally 65%, 70%, 75%, 80%,85%, 90%, or 95% similar over a specified region), when compared andaligned for maximum correspondence over a comparison window, ordesignated region as measured using one of the following sequencecomparison algorithms or by manual alignment and visual inspection.Sequences are “substantially similar” to each other if they are at least20%, at least 25%, at least 30%, at least 35%, at least 40%, at least45%, at least 50%, or at least 55% similar to each other. Optionally,this similarly exists over a region that is at least about 50 aminoacids in length, or more typically over a region that is at least about100 to 500 or 1000 or more amino acids in length.

For sequence comparison, typically one sequence acts as a referencesequence, to which test sequences are compared. When using a sequencecomparison algorithm, test and reference sequences are entered into acomputer, subsequence coordinates are designated, if necessary, andsequence algorithm program parameters are designated. Default programparameters are commonly used, or alternative parameters can bedesignated. The sequence comparison algorithm then calculates thepercent sequence identities or similarities for the test sequencesrelative to the reference sequence, based on the program parameters.

A “comparison window,” as used herein, includes reference to a segmentof any one of the number of contiguous positions selected from the groupconsisting of from 20 to 600, usually about 50 to about 200, moreusually about 100 to about 150 in which a sequence may be compared to areference sequence of the same number of contiguous positions after thetwo sequences are optimally aligned. Methods of alignment of sequencesfor comparison are well known in the art. Optimal alignment of sequencesfor comparison can be conducted, for example, by the local homologyalgorithm of Smith and Waterman (Adv. Appl. Math. 2:482, 1970), by thehomology alignment algorithm of Needleman and Wunsch (J. Mol. Biol.48:443, 1970), by the search for similarity method of Pearson and Lipman(Proc. Natl. Acad. Sci. USA 85:2444, 1988), by computerizedimplementations of these algorithms (e.g., GAP, BESTFIT, FASTA, andTFASTA in the Wisconsin Genetics Software Package, Genetics ComputerGroup, 575 Science Dr., Madison, Wis.), or by manual alignment andvisual inspection (see, e.g., Ausubel et al., Current Protocols inMolecular Biology (1995 supplement)).

Algorithms suitable for determining percent sequence identity andsequence similarity are the BLAST and BLAST 2.0 algorithms, which aredescribed in Altschul et al. (Nuc. Acids Res. 25:3389-402, 1977), andAltschul et al. (J. Mol. Biol. 215:403-10, 1990), respectively. Softwarefor performing BLAST analyses is publicly available through the NationalCenter for Biotechnology Information (http://www.ncbi.nlm.nih.gov/).This algorithm involves first identifying high scoring sequence pairs(HSPs) by identifying short words of length W in the query sequence,which either match or satisfy some positive-valued threshold score Twhen aligned with a word of the same length in a database sequence. T isreferred to as the neighborhood word score threshold (Altschul et al.,supra). These initial neighborhood word hits act as seeds for initiatingsearches to find longer HSPs containing them. The word hits are extendedin both directions along each sequence for as far as the cumulativealignment score can be increased. Cumulative scores are calculatedusing, for nucleotide sequences, the parameters M (reward score for apair of matching residues; always >0) and N (penalty score formismatching residues; always <0). For amino acid sequences, a scoringmatrix is used to calculate the cumulative score. Extension of the wordhits in each direction are halted when: the cumulative alignment scorefalls off by the quantity X from its maximum achieved value; thecumulative score goes to zero or below, due to the accumulation of oneor more negative-scoring residue alignments; or the end of eithersequence is reached. The BLAST algorithm parameters W, T, and Xdetermine the sensitivity and speed of the alignment. The BLASTN program(for nucleotide sequences) uses as defaults a wordlength (W) of 11, anexpectation (E) or 10, M=5, N=−4 and a comparison of both strands. Foramino acid sequences, the BLASTP program uses as defaults a wordlengthof 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (seeHenikoff and Henikoff, Proc. Natl. Acad. Sci. USA 89:10915, 1989)alignments (B) of 50, expectation (E) of 10, M=5, N=−4, and a comparisonof both strands.

The BLAST algorithm also performs a statistical analysis of thesimilarity between two sequences (see, e.g., Karlin and Altschul, Proc.Natl. Acad. Sci. USA 90:5873-87, 1993). One measure of similarityprovided by the BLAST algorithm is the smallest sum probability (P(N)),which provides an indication of the probability by which a match betweentwo nucleotide or amino acid sequences would occur by chance. Forexample, a nucleic acid is considered similar to a reference sequence ifthe smallest sum probability in a comparison of the test nucleic acid tothe reference nucleic acid is less than about 0.2, typically less thanabout 0.01, and more typically less than about 0.001.

“Recombinant,” as used herein, refers to an amino acid sequence or anucleotide sequence that has been intentionally modified by recombinantmethods. By the term “recombinant nucleic acid” herein is meant anucleic acid, originally formed in vitro, in general, by themanipulation of a nucleic acid by endonucleases, in a form not normallyfound in nature. Thus an isolated, mutant glycosyltransferase nucleicacid, in a linear form, or an expression vector formed in vitro byligating DNA molecules that are not normally joined, are both consideredrecombinant for the purposes of this invention. It is understood thatonce a recombinant nucleic acid is made and reintroduced into a hostcell, it will replicate non-recombinantly, i.e., using the in vivocellular machinery of the host cell rather than in vitro manipulations;however, such nucleic acids, once produced recombinantly, althoughsubsequently replicated non-recombinantly, are still consideredrecombinant for the purposes of the invention. A “recombinant protein”is a protein made using recombinant techniques, i.e., through theexpression of a recombinant nucleic acid as depicted above.

The term “vector” refers to a piece of DNA, typically double-stranded,which may have inserted into it a piece of foreign DNA. The vector maybe, for example, of plasmid origin. Vectors contain “replicon”polynucleotide sequences that facilitate the autonomous replication ofthe vector in a host cell. Foreign DNA is defined as heterologous DNA,which is DNA not naturally found in the host cell, which, for example,replicates the vector molecule, encodes a selectable or screenablemarker, or encodes a transgene. The vector is used to transport theforeign or heterologous DNA into a suitable host cell. Once in the hostcell, the vector can replicate independently of or coincidental with thehost chromosomal DNA, and several copies of the vector and its insertedDNA can be generated. In addition, the vector can also contain thenecessary elements that permit transcription of the inserted DNA into anmRNA molecule or otherwise cause replication of the inserted DNA intomultiple copies of RNA. Some expression vectors additionally containsequence elements adjacent to the inserted DNA that increase thehalf-life of the expressed mRNA and/or allow translation of the mRNAinto a protein molecule. Many molecules of mRNA and polypeptide encodedby the inserted DNA can thus be rapidly synthesized.

The term “nucleotide,” in addition to referring to the naturallyoccurring ribonucleotide or deoxyribonucleotide monomers, shall hereinbe understood to refer to related structural variants thereof, includingderivatives and analogs, that are functionally equivalent with respectto the particular context in which the nucleotide is being used (e.g.,hybridization to a complementary base), unless the context clearlyindicates otherwise.

The term “nucleic acid” or “polynucleotide” refers to a polymer that canbe corresponded to a ribose nucleic acid (RNA) or deoxyribose nucleicacid (DNA) polymer, or an analog thereof. This includes polymers ofnucleotides such as RNA and DNA, as well as synthetic forms, modified(e.g., chemically or biochemically modified) forms thereof, and mixedpolymers (e.g., including both RNA and DNA subunits). Exemplarymodifications include methylation, substitution of one or more of thenaturally occurring nucleotides with an analog, internucleotidemodifications such as uncharged linkages (e.g., methyl phosphonates,phosphotriesters, phosphoamidates, carbamates, and the like), pendentmoieties (e.g., polypeptides), intercalators (e.g., acridine, psoralen,and the like), chelators, alkylators, and modified linkages (e.g., alphaanomeric nucleic acids and the like). Also included are syntheticmolecules that mimic polynucleotides in their ability to bind to adesignated sequence via hydrogen bonding and other chemicalinteractions. Typically, the nucleotide monomers are linked viaphosphodiester bonds, although synthetic forms of nucleic acids cancomprise other linkages (e.g., peptide nucleic acids as described inNielsen et al. (Science 254:1497-1500, 1991). A nucleic acid can be orcan include, e.g., a chromosome or chromosomal segment, a vector (e.g.,an expression vector), an expression cassette, a naked DNA or RNApolymer, the product of a polymerase chain reaction (PCR), anoligonucleotide, a probe, and a primer. A nucleic acid can be, e.g.,single-stranded, double-stranded, or triple-stranded and is not limitedto any particular length. Unless otherwise indicated, a particularnucleic acid sequence comprises or encodes complementary sequences, inaddition to any sequence explicitly indicated.

As used herein, the term “oligosaccharide” refers to a compoundcontaining at least two sugars covalently linked together.Oligosaccharides include disaccharides, trisaccharides,tetrasachharides, pentasaccharides, hexasaccharides, heptasaccharides,octasaccharides, and the like. Covalent linkages generally consist ofglycosidic linkages (i.e., C—O—C bonds) formed from the hydroxyl groupsof adjacent sugars. Linkages can occur between the 1-carbon and the4-carbon of adjacent sugars (i.e., a 1-4 linkage), the 1-carbon and the3-carbon of adjacent sugars (i.e., a 1-3 linkage), the 1-carbon and the6-carbon of adjacent sugars (i.e., a 1-6 linkage), or the 1-carbon andthe 2-carbon of adjacent sugars (i.e., a 1-2 linkage). A sugar can belinked within an oligosaccharide such that the anomeric carbon is in theα- or β-configuration. The oligosaccharides prepared according to themethods of the invention can also include linkages between carbon atomsother than the 1-, 2-, 3-, 4-, and 6-carbons.

“Acceptor sugar” refers a sugar that accepts the sugar being added. Forexample, the acceptor sugar can be an oligosaccharide, such as afucosylated oligosaccharide, that accepts a sialic acid or analogthereof.

“Donor substrate” refers to a compound having a nucleotide and the sugarthat is added to the acceptor, where the sugar and nucleotide arecovalently bound together. The sugar can be sialic acid or analogsthereof. The nucleotide can be any suitable nucleotide such as cytidinemonophosphate (CMP).

“Sialic acid aldolase” refers to an aldolase that prepares sialic acidusing pyruvate and N-acetyl mannose (ManNAc).

III. Glycosyltransferases

The present invention includes a variety of sialyltransferases withreduced sialidase and/or donor substrate hydrolysis activity.Sialyltransferases are one class of glycosyltransferases, enzymes thatcatalyze the transfer of a sugar from a nucleotide-sugar complex (donorsubstrate) to an acceptor, a mono, di or oligosaccharide.Sialyltransferases catalyze the transfer of N-acetylneuraminic acid, andanalogs thereof, from a sialic acid-nucleotide complex, the donorsubstrate, to the terminal sugar of the acceptor which can be amonosaccharide, an oligosaccharide, a glycolipid, a glycopeptide, or aglycoprotein. Representative sialyltransferases include, but are notlimited to, sialyltransferases in family EC 2.4.99, such asbeta-galactosamide alpha-2,6-sialyltransferase (EC 2.4.99.1),alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase (EC 2.4.99.3),beta-galactoside alpha-2,3-sialyltransferase (EC 2.4.99.4),N-acetyllactosaminide alpha-2,3-sialyltransferase (EC 2.4.99.6),alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase (EC 2.4.99.8);lactosylceramide alpha-2,3-sialyltransferase (EC 2.4.99.9). Thesialyltransferases of the present invention also include those of theCAZy GT80 family, or EC 2.4.99.4, drawn to alpha2-3 and alpha2-6sialyltransferases, as well as sialyltransferases in the GT29, GT30,GT38, GT42, GT52, and GT73 families. Representative GT80sialyltransferases include, but are not limited to, PmST1, Psp26ST,Vsp23ST, Pd26ST, P1ST6 JT-1, P1ST6 JT-2, Pp Pst3-1, Pp Pst3-2, Np23STand Hd0053. (See Glycobiology 201, 21(6), 716; J. Mol. Biol. 2003, 328,307; Annu. Rev. Biochem. 2008, 77, 521; Appl. Microbiol. Biotechnol.2012, 94, 887 for review of sialyltransferases.)

The glycosyltransferases of the present invention include those havingdecreased α2-3 sialidase or donor substrate hydrolysis activity comparedto a control glycosyltransferase. α2-3 sialidase activity refers to theback reaction starting from the product oligosaccharide, cleaving theglycosidic bond between the sugar from the donor substrate and theacceptor, resulting in the donor substrate and the acceptor.

In some embodiments, the glycosyltransferase can be anα2-3-sialyltransferase. The α2-3-sialyltransferases of the presentinvention can include sialyltransferases of Pasteurella multocida. Insome embodiments, the glycosyltransferases of the present invention canhave a motif in the sialyltransferase domain including at least one ofsialyltransferase motif A (YDDGS, corresponding to positions 139-143 ofPmST1 wild type, SEQ ID NO:13) and sialyltransferase motif B (KGH,corresponding to positions 309-311 of PmST1 wild type, SEQ ID NO:13).

The glycosyltransferases of the present invention can include apolypeptide having any suitable percent identity to the controlsequence. For example, the glycosyltransferases of the present inventioncan include a polypeptide having a percent sequence identity to thecontrol glycosyltransferase sequence of at least 20, 30, 40, 50, 55, 60,65, 70, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98 or at least 99%.In some embodiments, percent sequence identity can be at least 80%. Insome embodiments, percent sequence identity can be at least 90%. In someembodiments, percent sequence identity can be at least 95%. In someembodiments, the glycosyltransferase includes a polypeptide sequencehaving at least 80% sequence identity to SEQ ID NO:1.

In some embodiments, the isolated glycosyltransferase includes apolypeptide sequence of SEQ ID NO:3 (M120D), SEQ ID NO:5 (M120H), SEQ IDNO:7 (E247F), SEQ ID NO: 9 (R289Y) or SEQ ID NO: 11 (E247F/R289Y).

The precise length of glycosyltransferases can vary, so the preciseamino acid positions corresponding to each mutation can vary dependingon the particular control glycosyltransferase used. Amino acid andnucleic acid sequence alignment programs are readily available (see,e.g., those referred to supra) and, given the particular motifsidentified herein, serve to assist in the identification of the exactamino acids (and corresponding codons) for modification in accordancewith the present invention. The positions of several mutations are shownin the table below for the PmST1 wild type sequence (SEQ ID NO:13) andthe Δ24PmST1 (SEQ ID NO:1) sequence.

PmST1 wild type Δ24PmST1 Mutation (SEQ ID NO: 13) (SEQ ID No: 1) 1 M144DM120D 2 M144H M120H 3 E271F E247F 4 R313Y R289Y 5 E271F/R313YE247F/R289Y

The above table illustrates “correspondence” of an amino acid positionto a different sequence. For example, amino acid position 144 in thePmST1 wild type sequence (SEQ ID NO:13) corresponds to position 120 ofthe Δ24PmST1 sequence (SEQ ID NO: 1).

The control glycosyltransferases of the present invention includes anysuitable glycosyltransferase or sialyltransferase. Theglycosyltransferases of the present invention includes mutantscorresponding to any position of PmST1 wild type sequence (SEQ ID NO:13)and Δ24PmST1 (SEQ ID NO:1) (see Biochemistry 2006, 45(7), 2139, and2007, 46(21), 6288). For example, the glycosyltransferases of thepresent invention include, but are not limited to, mutants at at leastone of positions 120, 247 and 289 of Δ24PmST1 (SEQ ID NO:1). Otherglycosyltransferases include mutants at at least one of positions 144,271 and 313 of PmST1 wild type sequence (SEQ ID NO:13). The mutants caninclude any suitable amino acid other than the native amino acid. Forexample, the amino acid can be V, I, L, M, F, W, P, S, T, A, G, C, Y, N,Q, D, E, K, R, or H. In some embodiments, the controlglycosyltransferase can be the PmST1 wild type sequence (SEQ ID NO:13)or the Δ24PmST1 (SEQ ID NO:1). In some embodiments, the controlglycosyltransferase can be Δ24PmST1 (SEQ ID NO:1).

In some embodiments, the present invention provides an isolatedglycosyltransferase, wherein the amino acid of the glycosyltransferasecorresponding to position 120 of SEQ ID NO:1 is any amino acid otherthan M, the amino acid the glycosyltransferase corresponding to position247 of SEQ ID NO:1 is any amino acid other than E, or the amino acid theglycosyltransferase corresponding to position 289 of SEQ ID NO:1 is anyamino acid other than R. The glycosyltransferase of the presentinvention has decreased α2-3 sialidase or donor substrate hydrolysisactivity compared to a control glycosyltransferase, wherein the aminoacid of the control glycosyltransferase corresponding to position 120 ofSEQ ID NO:1 is M, the amino acid of the control glycosyltransferasecorresponding to position 247 of SEQ ID NO:1 is E, and the amino acid ofthe control glycosyltransferase corresponding to position 289 of SEQ IDNO:1 is R. Finally, the glycosyltransferase of the present invention canbe a member of the glycosyltransferase family 80 (GT80).

In some embodiments, the isolated glycosyltransferase has decreased α2-3sialidase activity, and includes at least one of the amino acidcorresponding to position 247 of SEQ ID NO:1 is any amino acid otherthan E, and the amino acid corresponding to position 289 of SEQ ID NO:1is any amino acid other than R. Decreased α2-3 sialidase activity can bemeasured by the ratio of α2-3 sialidase activity for the controlglycosyltransferase to the α2-3 sialidase activity of the isolatedglycosyltransferase. The ratio can be at least 2:1, 3:1, 4:1, 5:1, 10:1,20:1, 30:1, 40:1, 50:1, 100:1, 200:1, 300:1, 400:1, 500:1 or at least1000:1. In some embodiments, the ratio is at least 5:1. In someembodiments, the ratio is at least 10:1. In some embodiments, the ratiois at least 100:1. In some embodiments, the ratio is at least 1000:1.

In some embodiments, the isolated glycosyltransferase having decreasedα2-3 sialidase activity includes the amino acid corresponding toposition 247 of SEQ ID NO:1 is any amino acid other than E, and theamino acid corresponding to position 289 of SEQ ID NO:1 is any aminoacid other than R.

In some embodiments, the isolated glycosyltransferase having decreasedα2-3 sialidase activity includes the amino acid corresponding toposition 117 of SEQ ID NO:1 is D or E. In some embodiments, the isolatedglycosyltransferase having decreased α2-3 sialidase activity includesthe amino acid corresponding to position 117 of SEQ ID NO:1 is A, G, V,L or I. In some embodiments, the isolated glycosyltransferase havingdecreased α2-3 sialidase activity includes the amino acid correspondingto position 287 of SEQ ID NO:1 is H, K, R, W or F.

Other glycosyltransferases of the present invention have decreased donorsubstrate hydrolysis activity. Decreased donor substrate hydrolysisactivity can be measured by the ratio of donor substrate hydrolysisactivity for the control glycosyltransferase to the donor substratehydrolysis activity of the isolated glycosyltransferase. The ratio canbe at least 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1 or at least 10:1. Insome embodiments, the isolated glycosyltransferase has decreased donorsubstrate hydrolysis activity, wherein the amino acid corresponding toposition 120 of SEQ ID NO:1 is any amino acid other than M. In someembodiments, the ratio of donor substrate hydrolysis activity for thecontrol α2-3 sialidase to the donor substrate hydrolysis activity of theisolated glycosyltransferase is at least 2:1.

In some embodiments, the amino acid corresponding to position 120 of SEQID NO:1 can be any amino acid of V, I, L, F, W, P, S, T, A, G, C, Y, N,Q, D, E, K, R, or H. In some embodiments, the amino acid correspondingto position 120 of SEQ ID NO:1 can be any amino acid of D, E, H, K or R.In some embodiments, the amino acid corresponding to position 120 of SEQID NO:1 can be any amino acid of D or H. In some embodiments, the aminoacid corresponding to position 120 of SEQ ID NO:1 can be amino acid D.In some embodiments, the amino acid corresponding to position 120 of SEQID NO:1 can be amino acid H.

In some embodiments, the amino acid corresponding to position 247 of SEQID NO:1 can be any amino acid of V, I, L, M, F, W, P, S, T, A, G, C, Y,N, Q, D, K, R, or H. In some embodiments, the amino acid correspondingto position 247 of SEQ ID NO:1 can be any amino acid of F, Y or W. Insome embodiments, the amino acid corresponding to position 247 of SEQ IDNO:1 can be amino acid F.

In some embodiments, the amino acid corresponding to position 289 of SEQID NO:1 can be any amino acid of V, I, L, M, F, W, P, S, T, A, G, C, Y,N, Q, D, E, K, and H. In some embodiments, the amino acid correspondingto position 289 of SEQ ID NO:1 can be any amino acid of Y, F or W. Insome embodiments, the amino acid corresponding to position 289 of SEQ IDNO:1 can be amino acid Y.

The glycosyltransferases of the present invention can have one or moremutations. In some embodiments, the glycosyltransferase includes theamino acid corresponding to position 247 of SEQ ID NO:1 can be any aminoacid of F, Y or W, and the amino acid corresponding to position 289 ofSEQ ID NO:1 can be any amino acid of Y, F or W. In some embodiments, theamino acid corresponding to position 247 of SEQ ID NO:1 can be aminoacid F, and the amino acid corresponding to position 289 of SEQ ID NO:1can be amino acid Y.

In some embodiments, the isolated glycosyltransferase can be the aminoacid corresponding to position 120 of SEQ ID NO:1 is D, E, H, K or R,the amino acid corresponding to position 247 of SEQ ID NO:1 is F, Y orW, or the amino acid corresponding to position 289 of SEQ ID NO:1 is Y,F or W. In some embodiments, the isolated glycosyltransferase can be theamino acid corresponding to position 120 of SEQ ID NO:1 is D or H, theamino acid corresponding to position 247 of SEQ ID NO:1 is F, or theamino acid corresponding to position 289 of SEQ ID NO:1 is Y.

The glycosyltransferases of the present invention can be constructed bymutating the DNA sequences that encode the corresponding unmodifiedglycosyltransferase (e.g., a wild-type glycosyltransferase or acorresponding variant from which the glycosyltransferase of theinvention is derived), such as by using techniques commonly referred toas site-directed mutagenesis. Nucleic acid molecules encoding theunmodified form of the glycosyltransferase can be mutated by a varietyof techniques well-known to one of ordinary skill in the art. (See,e.g., PCR Strategies (M. A. Innis, D. H. Gelfand, and J. J. Sninskyeds., 1995, Academic Press, San Diego, Calif.) at Chapter 14; PCRProtocols: A Guide to Methods and Applications (M. A. Innis, D. H.Gelfand, J. J. Sninsky, and T. J. White eds., Academic Press, N Y,1990).

By way of non-limiting example, the two primer system, utilized in theTransformer Site-Directed Mutagenesis kit from Clontech, may be employedfor introducing site-directed mutants into a polynucleotide encoding anunmodified form of the glycosyltransferase. Following denaturation ofthe target plasmid in this system, two primers are simultaneouslyannealed to the plasmid; one of these primers contains the desiredsite-directed mutation, the other contains a mutation at another pointin the plasmid resulting in elimination of a restriction site. Secondstrand synthesis is then carried out, tightly linking these twomutations, and the resulting plasmids are transformed into a mutS strainof E. coli. Plasmid DNA is isolated from the transformed bacteria,restricted with the relevant restriction enzyme (thereby linearizing theunmutated plasmids), and then retransformed into E. coli. This systemallows for generation of mutations directly in an expression plasmid,without the necessity of subcloning or generation of single-strandedphagemids. The tight linkage of the two mutations and the subsequentlinearization of unmutated plasmids result in high mutation efficiencyand allow minimal screening. Following synthesis of the initialrestriction site primer, this method requires the use of only one newprimer type per mutation site. Rather than prepare each positionalmutant separately, a set of “designed degenerate” oligonucleotideprimers can be synthesized in order to introduce all of the desiredmutations at a given site simultaneously. Transformants can be screenedby sequencing the plasmid DNA through the mutagenized region to identifyand sort mutant clones. Each mutant DNA can then be restricted andanalyzed by electrophoresis, such as for example, on a MutationDetection Enhancement gel (Mallinckrodt Baker, Inc., Phillipsburg, N.J.)to confirm that no other alterations in the sequence have occurred (byband shift comparison to the unmutagenized control). Alternatively, theentire DNA region can be sequenced to confirm that no additionalmutational events have occurred outside of the targeted region.

Verified mutant duplexes in pET (or other) overexpression vectors can beemployed to transform E. coli such as, e.g., strain E. coli BL21 (DE3)pLysS, for high level production of the mutant protein, and purificationby standard protocols. The method of FAB-MS mapping, for example, can beemployed to rapidly check the fidelity of mutant expression. Thistechnique provides for sequencing segments throughout the whole proteinand provides the necessary confidence in the sequence assignment. In amapping experiment of this type, protein is digested with a protease(the choice will depend on the specific region to be modified since thissegment is of prime interest and the remaining map should be identicalto the map of unmutated protein). The set of cleavage fragments isfractionated by, for example, microbore HPLC (reversed phase or ionexchange, again depending on the specific region to be modified) toprovide several peptides in each fraction, and the molecular weights ofthe peptides are determined by standard methods, such as FAB-MS. Thedetermined mass of each fragment are then compared to the molecularweights of peptides expected from the digestion of the predictedsequence, and the correctness of the sequence quickly ascertained. Sincethis mutagenesis approach to protein modification is directed,sequencing of the altered peptide should not be necessary if the MS dataagrees with prediction. If necessary to verify a changed residue,CAD-tandem MS/MS can be employed to sequence the peptides of the mixturein question, or the target peptide can be purified for subtractive Edmandegradation or carboxypeptidase Y digestion depending on the location ofthe modification.

Recombinant Nucleic Acids

Mutant glycosyltransferases with at least one amino acid substituted canbe generated in various ways. In the case of amino acids located closetogether in the polypeptide chain, they may be mutated simultaneouslyusing one oligonucleotide that codes for all of the desired amino acidsubstitutions. If however, the amino acids are located some distancefrom each other (separated by more than ten amino acids, for example) itis more difficult to generate a single oligonucleotide that encodes allof the desired changes. Instead, one of two alternative methods may beemployed. In the first method, a separate oligonucleotide is generatedfor each amino acid to be substituted. The oligonucleotides are thenannealed to the single-stranded template DNA simultaneously, and thesecond strand of DNA that is synthesized from the template will encodeall of the desired amino acid substitutions. An alternative methodinvolves two or more rounds of mutagenesis to produce the desiredmutant. The first round is as described for the single mutants: DNAencoding the unmodified glycosyltransferase is used for the template, anoligonucleotide encoding the first desired amino acid substitution(s) isannealed to this template, and the heteroduplex DNA molecule is thengenerated. The second round of mutagenesis utilizes the mutated DNAproduced in the first round of mutagenesis as the template. Thus, thistemplate already contains one or more mutations. The oligonucleotideencoding the additional desired amino acid substitution(s) is thenannealed to this template, and the resulting strand of DNA now encodesmutations from both the first and second rounds of mutagenesis. Thisresultant DNA can be used as a template in a third round of mutagenesis,and so on. Alternatively, the multi-site mutagenesis method of Seyfang &Jin (Anal. Biochem. 324:285-291. 2004) may be utilized.

Accordingly, also provided are recombinant nucleic acids, optionallyisolated, encoding any of the glycosyltransferases of the presentinvention (e.g., glycosyltransferases comprising any of SEQ ID NOs:4, 6,8, 10 and 12). Using a nucleic acid of the present invention, encoding aglycosyltransferase of the invention, a variety of vectors can be made.Any vector containing replicon and control sequences that are derivedfrom a species compatible with the host cell can be used in the practiceof the invention. Generally, expression vectors include transcriptionaland translational regulatory nucleic acid regions operably linked to thenucleic acid encoding the mutant glycosyltransferase. The term “controlsequences” refers to DNA sequences necessary for the expression of anoperably linked coding sequence in a particular host organism. Thecontrol sequences that are suitable for prokaryotes, for example,include a promoter, optionally an operator sequence, and a ribosomebinding site. In addition, the vector may contain a PositiveRetroregulatory Element (PRE) to enhance the half-life of thetranscribed mRNA (see Gelfand et al. U.S. Pat. No. 4,666,848). Thetranscriptional and translational regulatory nucleic acid regions willgenerally be appropriate to the host cell used to express theglycosyltransferase. Numerous types of appropriate expression vectors,and suitable regulatory sequences are known in the art for a variety ofhost cells. In general, the transcriptional and translational regulatorysequences may include, e.g., promoter sequences, ribosomal bindingsites, transcriptional start and stop sequences, translational start andstop sequences, and enhancer or activator sequences. In typicalembodiments, the regulatory sequences include a promoter andtranscriptional start and stop sequences. Vectors also typically includea polylinker region containing several restriction sites for insertionof foreign DNA. In certain embodiments, “fusion flags” are used tofacilitate purification and, if desired, subsequent removal of tag/flagsequence, e.g., “His-Tag”. However, these are generally unnecessary whenpurifying an thermoactive and/or thermostable protein from a mesophilichost (e.g., E. coli) where a “heat-step” may be employed. Theconstruction of suitable vectors containing DNA encoding replicationsequences, regulatory sequences, phenotypic selection genes, and themutant glycosyltransferase of interest are prepared using standardrecombinant DNA procedures. Isolated plasmids, viral vectors, and DNAfragments are cleaved, tailored, and ligated together in a specificorder to generate the desired vectors, as is well-known in the art (see,e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual (ColdSpring Harbor Laboratory Press, New York, N.Y., 2nd ed. 1989)). In someembodiments, the present invention provides a recombinant nucleic acidencoding an isolated glycosyltransferase of the present invention.

Host Cells

In certain embodiments, the expression vector contains a selectablemarker gene to allow the selection of transformed host cells. Selectiongenes are well known in the art and will vary with the host cell used.Suitable selection genes can include, for example, genes coding forampicillin and/or tetracycline resistance, which enables cellstransformed with these vectors to grow in the presence of theseantibiotics.

In one aspect of the present invention, a nucleic acid encoding aglycosyltransferase of the invention is introduced into a cell, eitheralone or in combination with a vector. By “introduced into” orgrammatical equivalents herein is meant that the nucleic acids enter thecells in a manner suitable for subsequent integration, amplification,and/or expression of the nucleic acid. The method of introduction islargely dictated by the targeted cell type. Exemplary methods includeCaPO₄ precipitation, liposome fusion, LIPOFECTIN®, electroporation,viral infection, and the like.

In some embodiments, prokaryotes are used as host cells for the initialcloning steps of the present invention. Other host cells include, butare not limited to, eukaryotic (e.g., mammalian, plant and insectcells), or prokaryotic (bacterial) cells. Exemplary host cells include,but are not limited to, Escherichia coli, Saccharomyces cerevisiae,Pichia pastoris, Sf9 insect cells, and CHO cells. They are particularlyuseful for rapid production of large amounts of DNA, for production ofsingle-stranded DNA templates used for site-directed mutagenesis, forscreening many mutants simultaneously, and for DNA sequencing of themutants generated. Suitable prokaryotic host cells include E. coli K12strain 94 (ATCC No. 31,446), E. coli strain W3110 (ATCC No. 27,325), E.coli K12 strain DG116 (ATCC No. 53,606), E. coli X1776 (ATCC No.31,537), and E. coli B; however many other strains of E. coli, such asHB101, JM101, NM522, NM538, NM539, and many other species and genera ofprokaryotes including bacilli such as Bacillus subtilis, otherenterobacteriaceae such as Salmonella typhimurium or Serratia marcesans,and various Pseudomonas species can all be used as hosts. Prokaryotichost cells or other host cells with rigid cell walls are typicallytransformed using the calcium chloride method as described in section1.82 of Sambrook et al., supra. Alternatively, electroporation can beused for transformation of these cells. Prokaryote transformationtechniques are set forth in, for example Dower, in Genetic Engineering,Principles and Methods 12:275-296 (Plenum Publishing Corp., 1990);Hanahan et al., Meth. Enzymol., 204:63, 1991. Plasmids typically usedfor transformation of E. coli include pBR322, pUCI8, pUCI9, pUCI18,pUC119, and Bluescript M13, all of which are described in sections1.12-1.20 of Sambrook et al., supra. However, many other suitablevectors are available as well.

In some embodiments, the glycosyltransferases of the present inventionare produced by culturing a host cell transformed with an expressionvector containing a nucleic acid encoding the glycosyltransferase, underthe appropriate conditions to induce or cause expression of theglycosyltransferase. Methods of culturing transformed host cells underconditions suitable for protein expression are well-known in the art(see, e.g., Sambrook et al., supra). Suitable host cells for productionof the glycosyltransferases from lambda pL promoter-containing plasmidvectors include E. coli strain DG116 (ATCC No. 53606) (see U.S. Pat. No.5,079,352 and Lawyer, F. C. et al., PCR Methods and Applications2:275-87, 1993, which are both incorporated herein by reference).Following expression, the glycosyltransferase can be harvested andisolated. Methods for purifying the thermostable glycosyltransferase aredescribed in, for example, Lawyer et al., supra. In some embodiments,the present invention provides a cell including a recombinant nucleicacid of the present invention. In some embodiments, the cell can beprokaryotes, eukaryotes, mammalian, plant, bacteria or insect cells.

IV. Methods of Making Oligosaccharides

The glycosyltransferases of the present invention can be used to prepareoligosaccharides, specifically to add N-acetylneuraminic acid (Neu5Ac),other sialic acids, and analogs thereof, to a monosaccharide, anoligosaccharide, a glycolipid, a glycopeptide, or a glycoprotein. Asshown in FIG. 5, the glycosyltransferase PmST1, catalyzes the additionof CMP-Neu5Ac to a fucosylated oligosaccharide by transferring theNeu5Ac to the oligosaccharide.

In some embodiments, the present invention provides a method ofpreparing an oligosaccharide, the method including forming a reactionmixture including an acceptor sugar, a donor substrate containing asugar moiety and a nucleotide, and the glycosyltransferase of thepresent invention, under conditions sufficient to transfer the sugarmoiety from the donor substrate to the acceptor sugar, thereby formingthe oligosaccharide.

The acceptor sugar can be any suitable oligosaccharide, glycolipid,glycopeptide, or glycoprotein. When the acceptor sugar is anoligosaccharide, any suitable oligosaccharide can be used. For example,the acceptor sugar can be Galβ1-4GlcNAcαOR, wherein R can H, a sugar oran oligosaccharide. Alternatively, the acceptor sugar can befucosylated, such as Galβ1-4(Fucα1-3)GlcNAcαOR (Lewis^(x)βOR orLe^(x)βOR) wherein R can H, a sugar or an oligosaccharide.

The donor substrate includes a nucleotide and sugar. Any nucleotide canbe used, include, but are not limited to, adenine, guanine, cytosine,uracil and thymine nucleotides with one, two or three phosphate groups.In some embodiments, the nucleotide can be cytidine monophosphate (CMP).The sugar can be any suitable sugar. When the glycosyltransferase is asialyltransferase, the sugar can be N-acetylneuraminic acid or Neu5Ac,other sialic acids and analogs thereof. Sialic acid is a general termfor N- and O-substituted derivatives of neuraminic acid, and includes,but is not limited to, N-acetyl (Neu5Ac) or N-glycolyl (Neu5Gc)substitutions, as well as O-substitutions including acetyl, lactyl,methyl, sulfate and phosphate, among others. In some embodiments, thesialic acid can be a compound of the formula:

wherein R¹ can be H, OH, N₃, NHC(O)Me, NHC(O)CH₂OH, NHC(O)CH₂N₃,NHC(O)OCH₂C═CH₂, NHC(O)CH₂F, NHC(O)CH₂NHCbz, NHC(O)CH₂OC(O)Me, orNHC(O)CH₂OBn; and R², R³, and R⁴ can be independently selected from H,OH, N₃, OMe, F, OSO₃ ⁻, OPO₃H⁻, or OC(O)Me. In some embodiments, thedonor substrate can be CMP-Neu5Ac. Other donor substrates are useful inthe methods of the present invention. In other embodiments, the sialicacid can be a compound of the formula:

Any glycosyltransferase of the present invention can be used in themethods of the present invention. In some embodiments, theglycosyltransferase can include a polypeptide sequence such as SEQ IDNO:3. (M120D), SEQ ID NO:5 (M120H), SEQ ID NO:7 (E247F), SEQ ID NO:9(R289Y) or SEQ ID NO:11 (E247F/R289Y). In some embodiments, theglycosyltransferase can include a polypeptide sequence such as SEQ IDNO:3 (M120D) or SEQ ID NO:5 (M120H). In some embodiments, theglycosyltransferase can include a polypeptide sequence such as SEQ IDNO:7 (E247F), SEQ ID NO:9 (R289Y) or SEQ ID NO:11 (E247F/R289Y). Theglycosyltransferases can be, for example, purified, secreted by a cellpresent in the reaction mixture, or can catalyze the reaction within acell expressing the glycosyltransferase.

In another aspect of the present invention, reaction mixtures areprovided comprising the glycosyltransferases as described herein. Thereaction mixtures can further comprise reagents for use in glycosylationtechniques. For example, in certain embodiments, the reaction mixturescomprise a buffer, salts (e.g., Mn²⁺, Mg²⁺), and labels (e.g.,fluorophores).

The donor substrate can be prepared prior to preparation of theoligosaccharide, or prepared in situ immediately prior to preparation ofthe oligosaccharide. In some embodiments, the method of the presentinvention also includes forming a reaction mixture including aCMP-sialic acid synthetase, cytidine triphosphate, andN-acetylneuraminic acid (Neu5Ac) or a Neu5Ac analog, under conditionssuitable to form the CMP-Neu5Ac or CMP-Neu5Ac analog. In someembodiments, the step of forming the donor substrate and the step offorming the oligosaccharide are performed in one pot.

In some embodiments, the sugar is prepared separately prior to use inthe methods of the present invention. Alternatively, the sugar can beprepared in situ immediately prior to use in the methods of the presentinvention. In some embodiments, the method also includes forming areaction mixture including a sialic acid aldolase, pyruvic acid orderivatives thereof, and N-acetylmannosamine or derivatives thereof,under conditions suitable to form the Neu5Ac or Neu5Ac analog. In someembodiments, the step of forming the sugar, the step of forming thedonor substrate and the step of forming the oligosaccharide areperformed in one pot.

The oligosaccharide prepared by the method of the present invention canbe any suitable oligosaccharide, glycolipid or glycoprotein. Forexample, the oligosaccharide can be an α2-3-linkedsialyloligosaccharide. In some embodiments, the oligosaccharide can be afucosylated oligosaccharide. In some embodiments, the oligosaccharidecan be Neu5Acα2-3Galβ1-4(Fucα1-3)GlcNAcαOR (Sia-Lewis^(x)βOR orSLe^(x)βOR) wherein R can be H, a monosaccharide, or an oligosaccharide.In some embodiments, the oligosaccharide can beNeu5Acα2-3Galβ1-4GlcNAcαOR, wherein R can H, a monosaccharide, or anoligosaccharide.

V. EXAMPLES Example 1. Decreasing the Sialidase Activity ofMultifunctional Pasteurella multocida Alpha2-3-Sialyltransferase 1(PmST1) by Site-Directed Mutagenesis Methods

Materials.

Escherichia coli BL21 (DE3) was from Invitrogen (Carlsbad, Calif., USA).Ni²⁺-NTA agarose (nickel-nitrilotriacetic acid agarose) and QIAprep spinminiprep kit were from Qiagen (Valencia, Calif., USA). Bicinchoninicacid (BCA) protein assay kit was from Pierce Biotechnology, Inc.(Rockford, Ill.). QuikChange Multi Site-Directed Mutagenesis Kit wasfrom Agilent Technologies company/Stratagene (Santa Clara, Calif.).

Site-Directed Mutagenesis.

Site-directed mutagenesis was carried out using the QuikChangemulti-site-directed mutagenesis kit from Stratagene according to themanufacturer's protocol. The primers used were5′ACCGGCACGACAACTTGGTTTGGAAATACCGATGTGCG3′ for E271F and 5′ATCTACTTTAAAGGGCATCCTTATGGTGGTGAAATTAATGACTAC3′ for R313Y. The sites ofmutations are underlined.

Protein Expression and Purification.

The plasmids containing the mutant genes were transformed into E. coliBL21 (DE3). The E. coli cells were cultured in LB-rich media (10 g L⁻¹tryptone, 5 g L yeast extract, and 10 g L⁻¹NaCl) supplemented withampicillin (100 μg mL⁻¹). Overexpression of the mutant proteins wasachieved by adding 0.1 mM of isopropyl-1-thio-β-D-galactopyranoside(IPTG) to the E. coli culture when its OD₆₀₀=reached 0.8. The incubationof the induced culture was performed at 37° C. for 3 h with vigorousshaking at 250 rpm in a C25KC incubator shaker (New BrunswickScientific, Edison, N.J.).

His₆-tagged mutant proteins were purified from the cell lysate. Toobtain the cell lysate, the cell pellet harvested by centrifugation at4000 rpm for 2 h was resuspended in 20 mL (for cells obtained from oneliter culture) of lysis buffer (pH 8.0, 100 mM Tris-HCl containing 0.1%Triton X-100). To lyse the cells, lysozyme (50 μg mL⁻¹) and DNaseI (3 μgmL⁻¹) were then added to the resuspended cells followed by shaking at37° C. for 60 min. The cell lysate was obtained as the supernatant aftercentrifugation at 11,000 rpm for 20 min. Purification of His₆-taggedproteins from the lysate was achieved using an ÄKTA FPLC system (GEHealthcare) equipped with a HisTrap™ FF 5 mL column. The column waspre-equilibrated with 8 column volumes of the binding buffer (5 mMimidazole, 0.5 M NaCl, 50 mM Tris-HCl pH 7.5) prior to lysate loading.After the sample loading, the column was washed with 8 column volumes ofthe binding and washing buffer (40 mM imidazole, 0.5 M NaCl, 50 mMTris-HCl pH 7.5). Protein elution was carried out with 8 column volumesof the elute buffer (200 mM imidazole, 0.5 M NaCl, 50 mM Tris-HCl pH7.5). The fractions containing the purified enzyme were collected andstored at 4° C.

Kinetic assays. The kinetic assays for the sialidase activity wereperformed in duplicate in a total volume of 10 μL in MES buffer (100 mM,pH 5.5) containing different concentrations of Neu5Acα2-3LacβMU (0.4,1.0, 2.0, 4.0, 10.0, 20.0, 40.0, and 60.0 mM) and the mutant proteins(2.5 mg mL⁻¹ of D141A, 1.6 mg mL⁻¹ of E271F, 1 mg mL⁻¹ of R313Y, and 3.2mg mL⁻¹ of E271F/R313Y). All reactions were allowed to proceed at 37° C.for 60 min (D141A), 1 min (E271F), 25 min (R313Y), and 20 min(E271F/R313Y). The apparent kinetic parameters were obtained by fittingthe experimental data (the average values of duplicate assay results)into the Michaelis-Menten equation using Grafit 5.0.

To obtain the apparent kinetic parameters of LacβMU as the acceptor forthe α2-3-sialyltransferase activity, the kinetic assays were performedin duplicate in reaction mixtures of 10 μL containing Tris-HCl buffer(100 mM, pH 8.5), a fixed concentration of CMP-Neu5Ac (1 mM), differentconcentrations of LacβMU (0.2, 0.5, 1.0, 2.0, 5.0, and 9.0 mM) and themutant proteins (2 μg mL⁻¹ of E271F, 2 μg mL⁻¹ of R313Y, and 1.6 μg mL⁻¹of E271F/R313Y). All reactions were allowed to proceed at 37° C. for 5min (E271F), 7 min (R313Y), and 10 min (E271F/R313Y). The apparentkinetic parameters were obtained by fitting the experimental data (theaverage values of duplicate assay results) into the Michaelis-Mentenequation using Grafit 5.0.

To obtain the apparent kinetic parameters of CMP-Neu5Ac as the donor forthe α2-3-sialyltransferase activity, the kinetic assays were performedin duplicate in reaction mixtures of 10 μL containing Tris-HCl buffer(100 mM, pH 8.5), a fixed concentration of LacβMU (1 mM), differentconcentrations of CMP-Neu5Ac (0.1, 0.2, 0.5, 1.0, 2.0, 5.0, 10.0 and20.0 mM) and the mutant proteins (2 μg mL⁻¹ of E271F, 2 μg mL⁻¹ ofR313Y, and 1.6 μg mL⁻¹ of E271F/R313Y). All reactions were allowed toproceed at 37° C. for 2 min (E271F), 7 min (R313Y), and 5 min(E271F/R313Y). The apparent kinetic parameters were obtained by fittingthe experimental data (the average values of duplicate assay results)into the Michaelis-Menten equation using Grafit 5.0.

All the sialidase and α2-3-sialyltransferase assays were performed in anHPLC system. Reactions were stopped by adding 10 μL of ethanol. Afternecessary dilutions were performed to adjust the concentrations of thefluorescent-labeled compounds, the samples were then kept on ice untilaliquots of 8 μL were injected and analyzed by a Shimadzu LC-6AD systemequipped with a membrane on-line degasser, a temperature control unit,and a fluorescence detector (Shimadzu RF-10AXL). A reverse-phase PremierC18 column (250×4.6 mm i.d., 5 μm particle size, Shimadzu) protectedwith a C18 guard column cartridge was used. The mobile phase was 25%acetonitrile. The fluorescent compounds LacβMU and Neu5Acα2-3LacβMU weredetected by excitation at 325 nm and emission at 372 nm.

Acceptor substrate specificity assays by HPLC. Assays were performed induplicate in 20 mL of Tris-HCl buffer (100 mM, pH 8.5) containingCMP-Neu5Ac (1 mM), a fluorescent acceptor (1 mM), MgCl2 (20 mM), and anenzyme (2 □g mL-1, wild-type PmST1 or E271R/R313Y mutant). Reactionswere allowed to proceed for 5 min at 37° C. The 4-methylumbelliferone(MU)-labeled fluorescent acceptors and the products formed were detectedwith excitation at 325 nm and emission at 372 nm. The9-fluorenylmethylcarbamate (Fmoc)-labeled fluorescent acceptors and theproducts formed were detected with excitation at 262 nm and emission at313 nm. The 2-aminobenzoic acid (2AA)-labeled fluorescent acceptors andthe products formed were detected with excitation at 315 nm and emissionat 400 nm.

Stability Studies by HPLC.

Thermal stability studies were carried out by incubating wild-type PmST1or E271F/R313Y mutant solution (20 μg mL⁻¹) at 37° C. Samples werewithdrawn at various time intervals for enzyme activity assays.

Results

Kinetics of the α2-3-Sialidase Activity.

To test the involvement of D141 and H311 in the α2-3-sialidase activityof PmST1, the α2-3-sialidase activity of two previously obtained PmST1mutants, D141A and H311A, were evaluated using a fluorescentα2-3-sialoside, Neu5Acα2-3LacβMU, as the substrate. The α2-3-sialidaseactivity of H311A mutant was too low to obtain the kinetic data. For theα2-3-sialidase activity of D141A mutant, the K_(m) value (15±1 mM) wasabout the same as the wild-type PmST1 (24 mM), but its catalyticefficiency was about 7,300-fold lower than that of the wild-type PmST1mainly due to a much slower turnover number of the D141A mutant (Table1). These data indicated that both D141 and H311 are important for theα2-3-sialidase activity of PmST1.

TABLE 1 Apparent kinetic data for the α2-3-sialidase activity ofwild-type PmST1 (WT) and PmST1 mutants. k_(cat)/K_(m) K_(m) (mM) k_(cat)(s⁻¹) (s⁻¹ mM⁻¹) WT⁴ 24 2.3 × 10² 9.5  D141A 15 ± 1 (1.9 ± 0.1) × 10⁻²1.3 × 10⁻³ E271F  5.7 ± 0.9 0.92 ± 0.04 0.16 R313Y 51 ± 5 0.18 ± 0.013.6 × 10⁻³ E271F/R313Y (5.4 ± 0.6) × 10² 0.83 ± 0.08 1.5 × 10⁻³

Kinetics of the α2-3-Sialidase Activity of the Mutants E271F, R313Y, andE271F/R313Y.

The designed PmST1 mutants E271F, R313Y, and E271F/R313Y were expressedin E. coli using the same expression condition as the wild-type PmST1(100 mg L⁻¹ culture) and achieved a compatible level of expression (90mg L⁻¹ culture). Similar to the wild-type PmST1, one-step Ni²⁺-columnpurification was sufficient to provide pure protein (>99%) of themutants.

The kinetic assays for the α2-3-sialidase activity of the mutants E271F,R313Y, and E271F/R313Y using a fluorescent 4-methylumbelliferylsialoside, Neu5Acα2-3LacβMU, as the substrate (Table 1) indicated thatE271F mutation decreased the α2-3-sialidase activity of PmST1 about59-fold which was mainly caused by a 250-fold decrease in the turnovernumber despite of a 4.2-fold decrease in the K_(m) value. As expected,the R313Y mutation at a site close to the critical H311 residue for theα2-3-sialidase activity of PmST1 caused a 2,639-fold decrease in thecatalytic efficiency (k_(cat)/K_(m)=0.0036 s⁻¹ mM⁻¹) compared to thewild-type PmST1 (k_(cat)/K_(m)=9.5 s⁻¹ mM⁻¹) mainly due to a(1,278-fold) decreased k_(cat) value and a 2-fold increased K_(m) value.The E271F/R313Y double mutant had the lowest α2-3-sialidase activity(k_(cat)/K_(m)=0.0015 s⁻¹ mM⁻¹) which was a 6,333-fold decrease comparedto the wild-type PmST1 due to a 22.5-fold increase in the K_(m) valueand a 277-fold decrease in the k_(cat) value.

Kinetics of the α2-3-Sialyltransferase Activity of the Mutants E271F,R313Y, and E271F/R313Y.

Kinetic assays (Table 2) for the α2-3-sialyltransferase activity ofmutants E271F, R313Y, and E271F/R313Y using LacI3MU as the fluorescentacceptor and CMP-Neu5Ac as the donor indicated that either E271F orR313Y mutation did not cause significant changes on either the K_(m) orthe k_(cat) value, leading to quite consistent catalytic efficiencies(k_(cat)/K_(m)=28-39 s⁻¹ mM⁻¹) compared to the wild-type PmST1(k_(cat)/K_(m)=34 s⁻¹ mM⁻¹).

TABLE 2 Apparent kinetic data for the α2-3-sialyltransferase activity ofwild-type PmST1 (WT) and PmST1 mutants. CMP-Neu5Ac LacβMU Enzymes K_(m)(mM) k_(cat) (s⁻¹) k_(cat)/K_(m) (s⁻¹ mM⁻¹) K_(m) (mM) k_(cat) (s⁻¹)k_(cat)/K_(m) (s⁻¹ mM⁻¹) WT⁴ 0.44 32 73 1.4 47 34 E271F 0.18 ± 0.01 26 ±1 1.4 × 10² 0.71 ± 0.12 28 ± 1 39 R313Y 0.62 ± 0.04 19 ± 1 30 0.67 ±0.05 19 ± 1 28 E271F/R313Y 0.34 ± 0.02 23 ± 1 69 0.54 ± 0.04 17 ± 1 32

Acceptor Substrate Specificities of Wild-Type PmST1 and E271F/R313YMutant.

Fluorescent glycans with different glycosidic linkages and variousmonosaccharide units, including Galβ1-4Glcβ, Galβ1-4GlcNAcβ,Galβ1-3GalNAcα, and Galβ1-3GlcNAcβ structures, were used to investigatethe acceptor substrate specificities of the wild-type PmST1 andE271F/R313Y mutant. As shown in Error! Reference source not found, theE271F/R313Y mutant exhibited similar or slightly higher activity thanthe wild-type PmST1 towards different acceptors. Therefore, the acceptorpromiscuity of PmST1 was not changed significantly by E271F and R313Ymutations.

Thermal Stabilities of Wild-Type PmST1 and E271F/R313Y Mutant.

Incubating the wild-type PmST1 and E271F/R313Y mutant at 37° C. for upto 2 hours did not decrease their activities significantly (Error!Reference source not found.). Therefore, both enzymes are consideredquite stable and mutation does not affect the thermal stability of thePmST1.

Example 2. A Sialyltransferase Mutant with Decreased Donor Hydrolysisand Reduced Sialidase Activities for Directly Sialylating Lewis^(x)Methods

Site-directed mutagenesis, expression and purification of PmST1 mutants.Site-directed mutagenesis was performed using the QuikChangemulti-site-directed mutagenesis kit from Stratagene according to themanufacturer's protocol. The primers used were 5′AATCTTTATGACGATGGCTCAGATGAATATGTTGATTTAGAAAAAG 3′ for M144D; 5′AATCTTTATGACGATGGCTCACATGAATATGTTGATTTAGAAAAAG 3′ for M144H; 5′ATCACGCTGTATTTAGATCCTGATTCCTTACCGGCATTAAATCAG 3′ for A35D; and 5′ATCACGCTGTATTTAGATCCTCATTCCTTACCGGCATTAAATCAG 3′ for A35H. Theexpression and purification of the mutants were performed as previouslydescribed for the WT PmST1.

Kinetics of the donor hydrolysis activity of PmST1 and mutants bycapillary electrophoresis analysis. The reactions were carried out induplicate in a total volume of 10 μL at 37° C. for 15 min (WT), 40 min(D141A), 20 min (H311A), or 15 min (M144D and M144H) in Tris-HCl buffer(200 mM, pH 8.5) containing CMP-Neu5Ac (1, 2, 5, 10, 20 and 40 mM) andan enzyme (WT, 4 μg mL⁻¹; D141A, 1500 μg mL⁻¹; H311A, 40 μg mL⁻¹; M144D,39 μg mL⁻¹; M144H, 5 μg mL⁻¹). The reactions were stopped by adding 104of pre-chilled ethanol. The mixtures were incubated on ice for 30 minand centrifuged at 13,000 rpm for 5 min. The supernatants were dilutedwith borate buffer (25 mM, pH 9.5) and aliquotes of 54 each wereinjected to a Beckman Coulter P/ACE™ MDQ Capillary Electrophoresissystem equipped with a capillary (60 cm×75 μm i.d.) and monitored at 254nm. The apparent kinetic parameters were obtained by fitting theexperimental data (the average values of duplicate assay results) intothe Michaelis-Menten equation using Grafit 5.0.

Kinetics of the α2-3-sialyltransferase activity of PmST1 mutants by HPLCanalysis. With LacβMU as the acceptor substrate, the reactions wereperformed in duplicate at 37° C. for 10 min (M144D) or 4 min (M144H) ina reaction mixture (10 μL) containing Tris-HCl (100 mM, pH 8.5), anenzyme (5 μg mL⁻¹), and different concentrations (0.2, 0.5, 1.0, 2.0,and 5.0 mM) of LacβMU with a fixed concentration (1 mM) of CMP-Neu5Ac ordifferent concentrations (0.2, 0.5, 1.0, 2.0, 5.0, and 10.0 mM) ofCMP-Neu5Ac with a fixed concentration (1 mM) of LacβMU. With Le^(x)βMUas the acceptor substrate, the reactions were carried out in duplicateat 37° C. for 9 min (M144D) or 10 min (M144H) in a reaction mixture (10μL) containing CAPSO (100 mM, pH 9.5), an enzyme (M144D, 39 μg mL⁻¹ orM144H, 5 μg mL⁻¹), and various concentrations of Le^(x)βMU (1.0, 5.0,10.0, 15.0, 25.0, and 35.0 mM) with a fixed concentration (1 mM) ofCMP-Neu5Ac or various concentrations (0.2, 0.5, 1.0, 2.0, 5.0, 10.0,20.0, and 40.0 mM) of CMP-Neu5Ac with a fixed concentration (1 mM) ofLe^(x)βMU. Reactions were stopped by adding 10 μL of pre-chilledethanol. The mixtures were incubated on ice for 30 min and centrifugedat 13,000 rpm for 5 min. The supernatants were diluted with 25%acetonitrile and kept on ice until aliquots of 8 μL were injected andanalyzed by the Shimadzu LC-6AD system equipped with a membrane on-linedegasser, a temperature control unit, and a fluorescence detector(Shimadzu RF-10AXL). A reverse-phase Premier C18 column (250×4.6 mmi.d., 5 μm particle size, Shimadzu) protected with a C18 guard columncartridge was used. The mobile phase was 25% acetonitrile. Thefluorophore (MU)-labeled compounds were detected by excitation at 325 nmand emission at 372 nm. The apparent kinetic parameters were obtained byfitting the experimental data (the average values of duplicate assayresults) into the Michaelis-Menten equation using Grafit 5.0.

Kinetics of the α2-3-Sialidase Activity of PmST1 Mutants.

The reactions were performed in duplicate in a total volume of 10 μL at37° C. for 60 min (M144D) or 15 min (M144H) in MES buffer (100 mM, pH5.5) containing Neu5Acα2-3LacβMU (0.4, 1, 2, 4, 10, 20, 40 and 60 mM)and an enzyme (M144H, 1.36 mg mL⁻¹ or M144D, 1.05 mg mL⁻¹). Sampletreatment after the reaction and analysis were carried out by HPLCsimilar to that described above for the α2-3-sialyltransferase assays.

The α2-3-Sialidase Activity Assays of PmST1 and Mutants.

The reactions were carried out in duplicate in a total volume of 10 μLat 37° C. for 20 hr in MES buffer (100 mM, pH 5.5) containingNeu5Acα2-3Le^(x)βMU (1 mM) and an enzyme (4 mg mL⁻¹). Aliquots of 1 μLwere withdrawn at 1 hr, 6 hr and 20 hr, and analyzed by HPLC asdescribed above for the α2-3-sialyltransferase assays.

Accession Codes.

The structure of PmST1 M144D mutant in complex with CMP-3F(a)-Neu5Ac wasdeposited with a PDB ID code 3S44.

Materials and Compound Characterization.

Chemicals were purchased and used without further purification. ¹H NMR(600 MHz) and ¹³C NMR (150 MHz) spectra were recorded on a Varian VNMRS600 MHz spectrometer or ¹H NMR (800 MHz) and ¹³C NMR (200 MHz) on aBruker 800 MHz spectrometer. High resolution electrospray ionization(ESI) mass spectra were obtained at the Mass Spectrometry Facility inthe University of California, Davis. Silica gel 60 Å was used for flashcolumn chromatography. Thin-layer chromatography (TLC) was performed onsilica gel plates using anisaldehyde sugar stain or 5% sulfuric acid inethanol stain for detection. Gel filtration chromatography was performedwith a column (100 cm×2.5 cm) packed with BioGel P-2 Fine resins.Pasteurella multocida sialic acid aldolase, 1 N. meningitidis CMP-sialicacid synthetase (NmCSS), 2 and wild-type PmST1 were expressed in E. coliand purified as described previously.

Crystallization and Structure Determination.

PmST1 M144D mutant in Tris-HCl buffer (20 mM, pH 7.5) was concentratedto 13 mg mL⁻¹, and CMP-3F(axial)Neu5Ac was added to a finalconcentration of 2 mM. Binary CMP-3F(axial)Neu5Ac crystals were grown byhanging drop with 3 μL of the sample mixed with an equal volume ofreservoir buffer [24% poly(ethylene glycol) 3350, 100 mM HEPES (pH 7.5),50 mM NaCl, and 0.4% Triton X-100]. Then, the binary crystals weresoaking with 10 mM of CMP-3F(axial)-Neu5Ac and 10 mM of Le^(x)βProN₃ inbuffer containing 26% poly (ethylene glycol) 3350, HEPES (100 mM, pH7.5), NaCl (100 mM), and 0.4% Triton X-100 for overnight. All crystalswere transferred to Paratone-N and frozen in a steam of nitrogen to 100K for data collection. Diffraction data were collected at the StanfordSynchrotron Radiation Lightsource to 1.45 Å resolution. Data wereprocessed with XDS and scaled with XSCALE (Table 3). The structure wassolved by Molecular Replacement using the program PHASER. Only theligand-free open conformation structure (PDB ID: 2EXO) was successful instructure determination. The model was displayed and adjusted with COOTand refined with REFMAC. Final data processing and refinement statisticsare shown in Table 3.

TABLE 3 X-Ray data collection and refinement statistics for PmST1M144D.^(d) unit cell dimensions a,b,c (Å), β 52.44, 61.57, 62.58, β =114.15° space group P2₁ no. of monomers per asymmetric unit 1 resolutionrange (Å)  25.0-1.45 (1.49-1.45) R_(sym) ^([a]) (%)  3.8 (47.4) <I>/σ<I>19.06 (2.58) no. of reflections 229,446 (16,432) no. of uniquereflections 63,327 (4,962) redundancy  3.6 (3.3) completeness (%)  98.1(98.2) R_(factor) ^([b]) (%) 18.7 R_(free) ^([c]) (%) 21.5 no. ofprotein atoms 3,197 no. of CMP atoms 21 no. of water atoms 431 meanB-factor (Å²) Protein, all atoms 14.8 Protein, main chain 13.4 Protein,side chain 16.2 CMP 20.1 water 25.8 rmsd from ideality bond distance (Å)0.0128 bond angle (deg) 1.429 ^([a])R_(merge) = [Σ_(h)Σ_(i)|I_(h) −I_(hi)|/Σ_(h)Σ_(i)I_(hi)] where I_(h) is the mean of I_(hi) observationsof reflection h. Numbers in parenthesis represent highest resolutionshell. ^([b])R-Factor and ^([c])R_(free) = Σ||F_(obs)| −|F_(calc)||/Σ|F_(obs)| × 100 for 95% of recorded data (R-Factor) or 5%data (R_(free)) ^(d)Protein Data Bank Accession codes: The structure ofPmST1 M144D mutant in complex with CMP-3F(a)-Neu5Ac was deposited with aPDB ID code 3S44.

NMR Analysis of WT PmST1 and M144D Mutant.

Enzymes were expressed in E. coli BL21 (DE3) using M9 media containing¹⁵NH₄Cl (1.0 g L⁻¹), Na₂HPO₄.7H₂O (12.66 g L⁻¹), KH₂PO₄ (3.0 g L⁻¹),NaCl (0.5 g L⁻¹), MgSO₄ (0.2 g CaCl₂ (50 μM), and glucose (0.3%).Expressions were induced by adding 0.5 mM of isopropylβ-D-1-thiogalactopyranoside (IPTG) and incubating at 37° C. for 4 hr.The purifications were performed as previously described for the WTPmST1. The purified enzymes were dialyzed with a phosphate buffer (10mM, pH 7.0). NMR samples of ¹⁵N-labeled WT and M144D PmST1 (˜0.7 mM)were prepared in 90%/10% of H₂O/D₂O containing 10 mM of phosphate (pH7.0) in the presence or the absence of saturating CMP. ¹⁵N-¹H HSQC NMRexperiments were performed at 37° C. on Bruker Avance III 800spectrometer with an Ultrashield Bruker magnet equipped with afour-channel interface, triple-resonance probe, and cryo-probe withZ-axis pulsed field gradients. The number of complex points andacquisition times were: 256, 180 ms (¹⁵N (F₁)); and, 512, 64 ms (¹H(F₂)). The NMR spectra were processed and analyzed using the software,NMRPipe.

Example 3. Preparation of Oligosaccharides

One-pot three-enzyme synthesis of SLe^(x)βProN₃ with different sialicacid forms. Le^(x)βProN₃ (20-25 mg),⁹ a sialic acid precursor (mannose,ManNAc, ManNGc or their derivatives, 1.5 equiv.), sodium pyruvate (5equiv.), and CTP (1.5 equiv.) were dissolved in Tris-HCl buffer (10 mL,100 mM, pH 7.5-8.5) containing MgCl₂ (20 mM) and appropriate amounts ofPm aldolase (0.5 mg), NmCSS (0.3-0.5 mg), and PmST1 mutant M144D(0.5-0.9 mg). The reactions were carried out by incubating the reactionmixture in an incubator shaker at 37° C. for 4-6 h. The productformation was monitored by TLC developed withEtOAc:MeOH:H₂O:HOAc=4:2:1:0.2 (by volume) and stained withp-anisaldehydesugar stain. When an optimal yield was achieved, the reaction wasstopped by adding the same volume (10 mL) of cold EtOH and incubation at4° C. for 30 min. The mixture was then centrifuged and the precipitateswere removed. The supernatant was concentrated, passed through a BioGelP-2 gel filtration column, and eluted with water to obtain partiallypurified product. A silica gel column was then used to obtain puresialylated products with EtOAc:MeOH:H₂O=6:2:1 (by volume).

NMR chemical shifts and HRMS data of SLe^(x)βProN₃ containing differentsialic acid forms synthesized by the one-pot three-enzyme system.

Neu5Acα2-3Le^(x)βProN₃ (1a).

33 mg, yield 93%. ¹H NMR (600 MHz, D₂O): δ 5.09 (d, 1H, J=4.2 Hz), 4.50(d, 1H, J=7.8 Hz), 4.07 (dd, 1H, J=10.4 and 3.2 Hz), 4.01-3.82 (m, 11H),3.74 (d, 1H, J=4.2 Hz), 3.66-3.59 (m, 9H), 3.56-3.50 (m, 4H), 3.36-3.30(m, 2H), 2.72 (dd, 1H, J=12.6 and 4.8 Hz), 2.01 (s, 3H), 2.00 (s, 3H),1.87 (m, 2H), 1.75 (t, 1H, J=12.3 Hz), 1.12 (d, 3H, J=6.6). ¹³C NMR (150MHz, D₂O): δ 175.20, 174.41, 174.05, 101.79, 101.15, 99.82, 98.76,75.81, 75.42, 75.07, 74.98, 73.51, 73.07, 72.07, 72.03, 69.42, 69.35,68.47, 68.28, 67.87, 67.47, 67.36, 66.84, 62.76, 61.64, 59.81, 55.98,51.86, 47.93, 39.95, 28.27, 22.39, 22.20, 15.43. HRMS (ESI) m/z calcdfor C₃₄H₅₇N₅O₂₃Na (M+Na) 926.3319, found 926.3342.

Neu5Gcα2-3Le^(x)βProN₃ (1b).

28 mg, yield 87%. ¹H NMR (600 MHz, D₂O): δ 5.13 (d, 1H, J=4.2 Hz),4.56-4.54 (m, 2H), 4.15 (s, 2H), 4.07 (dd, 1H, J=10.4 and 3.2 Hz),4.01-3.82 (m, 12H), 3.78-3.60 (m, 8H), 3.56-3.54 (m, 3H), 3.52 (dd, 1H,J=10.4 and 7.8 Hz), 3.36-3.30 (m, 2H), 2.78 (dd, 1H, J=12.6 and 4.8 Hz),2.06 (s, 3H), 1.87 (m, 2H), 1.75 (t, 1H, J=12.3 Hz), 1.19 (d, 3H,J=6.6). ¹³C NMR (150 MHz, D₂O): δ 175.73, 174.17, 173.84, 101.55,100.91, 99.62, 98.52, 75.59, 75.20, 74.83, 74.75, 73.30, 72.57, 71.84,69.20, 69.12, 69.10, 67.98, 67.65, 67.23, 67.13, 66.57, 66.61, 62.50,60.91, 59.79, 59.60, 55.75, 51.33, 47.71, 39.78, 28.04, 22.16, 15.20.HRMS (ESI) m/z calcd for C₃₄H₅₇N₅O₂₄Na (M+Na) 942.3291, found 942.3292.

Kdnα2-3Le^(x)βProN₃ (1c).

27 mg, yield 85%. ¹H NMR (600 MHz, D₂O): δ 5.04 (d, 1H, J=4.2 Hz),4.47-4.45 (m, 2H), 3.85 (dd, 1H, J=9.6 and 2.4 Hz), 3.81-3.62 (m, 10H),3.56 (d, 1H, J=4.0 Hz), 3.49-3.29 (m, 12H), 3.18-3.14 (m, 3H), 2.65 (dd,1H, J=12.6 and 4.8 Hz), 1.98 (s, 3H), 1.87 (m, 2H), 1.69 (t, 1H, J=12.3Hz), 1.10 (d, 3H, J=6.6). ¹³C NMR (150 MHz, D₂O): δ 174.36, 174.17,101.72, 101.09, 99.76, 98.74, 75.70, 75.35, 75.02, 74.93, 74.04, 73.43,72.26, 71.99, 70.32, 69.84, 69.34, 69.26, 67.79, 67.36, 67.28, 66.79,62.73, 61.60, 59.73, 55.91, 47.84, 39.51, 28.21, 22.31, 15.37. HRMS(ESI) m/z calcd for C₃₂H₅₄N₄O₂₃Na (M+Na) 885.3077, found 885.3103.

Neu5AcN₃α2-3Le^(x)βProN₃ (1d).

33 mg, yield 89%. ¹H NMR (800 MHz, D₂O): δ 5.06 (d, 1H, J=4.0 Hz),4.47-4.56 (m, 2H), 4.01 (s, 2H), 3.96-3.76 (m, 11H), 3.72-3.59 (m, 10H),3.54-3.45 (m, 3H), 3.47 (dd, 1H, J=10.4 and 7.8 Hz), 3.34-3.27 (m, 2H),2.71 (dd, 1H, J=12.6 and 4.8 Hz), 1.98 (s, 3H), 1.81 (m, 2H), 1.74 (t,1H, J=12.3 Hz), 1.10 (d, 3H, J=6.6). ¹³C NMR (200 MHz, D₂O): δ 174.43,174.09, 171.36, 101.75, 101.17, 99.82, 98.81, 75.79, 75.40, 75.08,74.99, 73.47, 72.74, 72.10, 72.06, 69.43, 69.33, 68.35, 68.19, 67.86,67.44, 67.35, 66.86, 62.72, 61.67, 59.79, 55.98, m 52.06, 51.92, 47.91,39.97, 28.28, 22.38, 15.44. HRMS (ESI) m/z calcd for C₃₄H₅₆N₈O₂₃Na(M+Na) 967.3356, found 967.3396.

KdnN₃α2-3Le^(x)βProN₃ (1e).

27 mg, yield 84%. ¹H NMR (600 MHz, D₂O): δ 5.11 (d, 1H, J=4.0 Hz), 4.54(d, 1H, J=8.0 Hz), 4.52 (d, 1H, J=8.0 Hz), 4.07 (dd, 1H, J=9.6 and 3.2Hz), 4.03-3.83 (m, 11H), 3.78 (d, 1H, J=3.2 Hz), 3.72-3.66 (m, 6H),3.60-3.49 (m, 5H), 3.38-3.35 (m, 3H), 2.75 (dd, 1H, J=12.6 and 4.8 Hz),2.04 (s, 3H), 1.83 (m, 2H), 1.78 (t, 1H, J=12.3 Hz), 1.17 (d, 3H,J=6.6). ¹³C NMR (150 MHz, D₂O): δ 174.15, 173.64, 101.49, 100.88, 99.60,98.52, 75.53, 75.16, 74.78, 74.73, 73.25, 72.77, 71.93, 71.80, 69.38,69.16, 69.08, 68.30, 67.61, 67.10, 66.59, 62.50, 62.46, 61.38, 59.57,55.73, 47.67, 39.50, 28.02, 22.13, 15.17. HRMS (ESI) m/z calcd forC₃₂H₅₃N₇O₂₂Na (M+Na) 910.3141, found 910.3137.

9-N₃-Neu5Acα2-3Le^(x)βProN₃ (1f).

28 mg, yield 91%. ¹H NMR (800 MHz, D₂O): δ 5.11 (d, 1H, J=4.0 Hz), 4.56(d, 1H, J=8.0 Hz), 4.51 (d, 1H, J=8.0 Hz), 4.03-4.02 (m, 2H), 3.98-3.85(m, 9H), 3.79 (d, 1H, J=3.2 Hz), 3.71-3.69 (m, 8H), 3.61-3.49 (m, 6H),3.40-3.36 (m, 3H), 2.77 (dd, 1H, J=12.6 and 4.8 Hz), 2.05 (s, 3H), 1.83(m, 2H), 1.79 (t, 1H, J=12.3 Hz), 1.17 (d, 3H, J=6.6). ¹³C NMR (200 MHz,D₂O): δ 174.90, 174.16, 173.74, 101.51, 100.88, 99.58, 98.50, 75.63,75.21, 74.81, 74.73, 73.24, 72.64, 72.42, 71.81, 70.39, 69.19, 69.09,68.70, 68.20, 67.61, 67.15, 67.11, 66.59, 61.38, 59.60, 55.72, 53.01,51.59, 47.68, 39.77, 28.02, 22.14, 15.18. HRMS (ESI) m/z calcd forC₃₄H₅₆N₈O₂₂Na (M+Na) 951.3407, found 910.3407.

9-O—Ac-Neu5Acα2-3Le^(x)βProN₃ (1g).

20 mg, yield 62%. ¹H NMR (600 MHz, D₂O): δ 5.12 (d, 1H, J=4.0 Hz),4.55-4.53 (m, 2H), 4.44 (dd, 1H, J=11.4 and 1.8 Hz), 4.20 (dd, 1H,J=11.4 and 6.6 Hz), 4.14-3.86 (m, 11H), 3.79 (d, 1H, J=3.0 Hz),3.74-3.65 (m, 8H), 3.58-3.56 (m, 2H), 3.54 (dd, 1H, J=9.6 and 7.8 Hz),3.41-3.36 (m, 2H), 2.78 (dd, 1H, J=12.6 and 4.8 Hz), 2.16 (s, 3H), 2.05(s, 6H), 1.85 (m, 2H), 1.81 (t, 1H, J=12.6 Hz), 1.18 (d, 3H, J=6.6). ¹³CNMR (150 MHz, D₂O): δ 174.18, 174.41, 174.00, 173.96, 101.80, 101.14,99.80, 98.78, 75.88, 75.53, 75.09, 74.80, 73.54, 72.89, 72.08, 69.75,69.57, 69.45, 69.37, 68.46, 68.37, 67.89, 67.37, 66.86, 65.98, 61.65,59.84, 55.99, 51.85, 47.60, 40.05, 28.29, 22.41, 22.23, 20.44, 15.45.HRMS (ESI) m/z calcd for C₃₆H₅₉N₅O₂₄Na (M+Na) 968.3448, found 968.3427.

9-O—Ac-Neu5Gcα2-3Le^(x)βProN₃ (1h).

21 mg, yield 64%. ¹H NMR (600 MHz, D₂O): δ 5.12 (d, 1H, J=4.0 Hz), 4.55(dd, 1H, J=7.8 and 4.2 Hz), 4.45 (m, 1H), 4.22-4.19 (m, 1H), 4.14 (s,2H), 4.13-3.79 (m, 13H), 3.73-3.66 (m, 8H), 3.61-3.59 (m, 2H), 3.55 (t,1H, J=7.8 Hz), 3.41-3.37 (m, 2H), 2.80 (dd, 1H, J=12.6 and 4.8 Hz), 2.16(s, 3H), 2.06 (s, 6H), 1.88-1.85 (m, 2H), 1.81 (t, 1H, J=12.6 Hz), 1.19(d, 3H, J=6.6). ¹³C NMR (150 MHz, D₂O): δ 175.93, 174.54, 174.41,174.01, 101.80, 101.15, 99.81, 99.77, 75.86, 75.53, 75.09, 75.00, 73.54,72.62, 72.09, 69.75, 69.63, 69.45, 69.37, 68.30, 68.23, 67.90, 67.36,66.86, 65.93, 61.65, 61.17, 59.83, 55.99, 51.54, 47.95, 40.10, 28.29,22.41, 20.44, 15.45. HRMS (ESI) m/z calcd for C₃₆H₅₉N₅O₂₄Na (M+Na)984.3397, found 984.3397.

Results and Discussion

Donor hydrolysis by PmST1 causes low yield sialylation of Le^(x). Inorder to understand why PmST1-catalyzed sialylation of Le^(x) resultedin low yields, time course studies were carried out using afluorescently labeled Le^(x) acceptor (4-methylumbelliferyl 13-Le^(x) orLe^(x)βMU) in a high performance liquid chromatography (HPLC) assay. Asshown in Error! Reference source not found, PmST1-catalyzed sialylationof Le^(x)βMU (1 mM) using one equivalent of donor CMP-Neu5Ac reached alow yield (1.1-1.3%) plateau quickly within 2 min. Every additional doseof donor substrate CMP-Neu5Ac (shown by arrows in Error! Referencesource not found.) increased the product formation which always reacheda plateau quickly. Monitoring the CMP-Neu5Ac consumption (% consumptionnumbers are shown in parentheses in Error! Reference source not found.)in the reaction mixture by capillary electrophoresis studies confirmed aquick consumption of CMP-Neu5Ac. These indicated that donor (CMP-Neu5Ac)hydrolysis activity of PmST1, where water molecules compete with thepoor Le^(x) acceptor for the consumption of sugar nucleotide(CMP-Neu5Ac) donor of the sialyltransferase (Error! Reference source notfound.), contributed significantly to the low yield of PmST1-catalyzedsialylation. In fact, donor hydrolysis has been observed in otherglycosyltransferase-catalyzed reactions that lead to lower syntheticyields. The donor hydrolysis were observed frequently inco-crystallization of glycosyltransferases with a corresponding sugarnucleotide donor where its sugar component was usually cleaved off andonly the hydrolyzed nucleotide was observed in the substrate bindingpocket of the enzyme. Therefore, inert donor derivatives ofglycosyltransferases have been commonly applied in the x-ray crystalstructure studies of glycosyltransferases. Two recent papers discussedthe donor hydrolysis activities of human blood group A and Bglycosyltransferases (GTA and GTB) which are Mn²⁺-dependent and theUDP-Gal hydrolysis activity of GTB is increased in the presence of anacceptor substrate analog. Nevertheless, the effect of donor hydrolysisof glycosyltransferases on glycosylation processes has not beeninvestigated in detail. In addition, no strategy has been reported forimproving the yields of glycosyltransferase-catalyzed reactions bydecreasing donor hydrolysis activity.

Asp141 and His311 influence PmST1 donor hydrolysis activity. As shown inTable 4, D141A mutation decreased the efficiency of CMP-Neu5Achydrolysis activity of PmST1 by 1,000-fold mainly due to the decrease inthe turnover number. H311A mutation also decreased the CMP-Neu5Achydrolysis activity by 16-fold, mainly contributed by a decreasedturnover number without affecting the binding affinity significantly.

TABLE 4 Apparent kinetics of the CMP-Neu5Ac hydrolysis activity of WTPmST1 and mutants. K_(m) (mM) k_(cat) (s⁻¹) k_(cat)/K_(m) (s⁻¹ mM⁻¹) WT1.5 ± 0.2 27 ± 1  18 ^(a)D141A 1.4 ± 0.2 (2.5 ± 0.1) × 10⁻² 1.8 × 10⁻²^(a)H311A 1.8 ± 0.2 2.1 ± 0.1 1.1 M144D 7.3 ± 0.5 6.5 ± 0.1 0.89 M144H13 ± 3  71 ± 6  5.5 ^(a)PmST1 D141A and H311A mutants were generatedpreviously. See, Ni, et al. (2006) Biochemistry 45, 2139-2148.

PmST1 Mutants with Decreased CMP-Neu5Ac Hydrolysis Activity.

As shown in Table 4, both M144D and M144H mutations decreased theefficiency of donor hydrolysis. M144D mutation decreased the efficiencyof donor hydrolysis by 20-fold due to a 4.9-fold increase of the K_(m)value and a 4.2-fold decrease of the k_(cat) value. M144H mutationcaused a less significant 3.3-fold decrease in the efficiency of donorhydrolysis due to a significant 8.7-fold increase in the K_(m) valuewhich is offset by a 2.6-fold increase in the k_(cat) value.

α2-3-Sialyltransferase Activities of PmST1 Mutants.

As shown in Table 5, when a good sialyltransferase acceptor4-methylumbelliferyl β-lactoside (LacβMU) was used, the M144D mutationdecreased the α2-3-sialyltransferase activity by 18-fold due to a 9-foldincrease of K_(m) value and a 2-fold decrease of k_(cat) value. When apoor sialyltransferase acceptor Le^(x)βMU was used, the M144D mutationdid not change the efficiency of the α2-3-sialyltransferase activity ofPmST1 significantly. In comparison, M144H mutation only decreased theα2-3-sialyltransferase activity weakly (1.3-fold) when LacβMU was usedas an acceptor and increased the efficiency of α2-3-sialyltransferaseactivity by 2.6-fold when Le^(x)3MU was used as an acceptor.

TABLE 5 Apparent kinetics of the α2-3-sialyltransferase activity of WTPmST1 and mutants. K_(m) (mM) k_(cat) (s⁻¹) k_(cat)/K_(m) (s⁻¹ mM⁻¹) WTM144D M144H WT M144D M144H WT M144D M144H LacβMU ^(a)1.4  12 ± 1  0.79 ±0.04 ^(a)47 22 ± 1  21 ± 1  ^(a)34 1.9 27 ^(b)CMP-Neu5Ac ^(a)0.44 0.30 ±0.05 0.81 ± 0.06 ^(a)32 1.9 ± 0.1 21 ± 1  ^(a)73 6.1 27 Le^(x)βMU 17 ±2  13 ± 2  8.1 ± 0.9 6.7 ± 0.3 4.0 ± 0.2 8.4 ± 0.3 0.38 0.32 1.0^(c)CMP-Neu5Ac 0.39 ± 0.03 2.1 ± 0.1  0.4 ± 0.05 0.55 ± 0.01 0.59 ± 0.010.93 ± 0.02 1.4 0.28 2.2 ^(a)Data are from Yu, H., et al. (2005) J. Am.Chem. Soc. 127, 17618-17619. ^(b)With LacβMU, ^(c)With Le^(x)βMU.

PmST1 M144D Mutant has a Decreased α2-3-Sialidase Activity.

M144D and M144H mutations also decreased the α2-3-sialidase activity ofPmST1 by 5588- and 594-fold respectively when Neu5Acα2-3LacβMU was usedas the sialidase substrate (Table 6). While the PmST1 M144D mutantshowed no sialidase activity when Neu5Acα2-3Le^(x)βMU was used as thesubstrate, PmST1 M144H has increased sialidase activity compared to theWT PmST1 using the SLe^(x) substrate. For example, the PmST1 M144Hmutant cleaved 10.0%, 24.5%, and 34.0% of Neu5Ac fromNeu5Acα2-3Le^(x)βMU in 1 h, 6 h, and 20 h, respectively. In comparison,WT PmST1 removed 2.0%, 7.0%, and 7.5% of Neu5Ac from Neu5Acα2-3Le^(x)βMUunder the same reaction conditions. The decreased α2-3-sialidaseactivity by M144D mutation allows the potential application of the PmST1M144D mutant in sialylation of glycoconjugates containing terminalgalactoside or Le^(x) where the decreased α2-3-sialidase activity hasthe most advantages as these reactions are challenging for promptmonitoring.

TABLE 6 Apparent kinetics of the α2-3-sialidase activity of WT PmST1,M144D, and M144H mutants using Neu5Acα2-3LacβMU as the sialidasesubstrate. K_(m) (mM) k_(cat) (s⁻¹) k_(cat)/K_(m) (s⁻¹ mM⁻¹) ^(a)WT^(a)24 ^(a)2.3 × 10² ^(a)9.5 M144D 20 ± 2  (3.5 ± 0.1) × 10⁻² 1.7 × 10⁻³M144H 1.7 ± 0.3 (2.7 ± 0.2) × 10⁻² 1.6 × 10⁻² ^(a)Data are from Yu, H.,et al. (2005) J. Am. Chem. Soc. 127, 17618-17619.

PmST1 M144D mutant has a similar expression level as the WT PmST1. ThePmST1 M144D mutation did not change the enzyme expression level in E.coli. About 98 mg of C-His₆-tagged PmST1 M144D protein can be routinelypurified from one liter of E. coli cell culture using Ni²⁺-affinitycolumn (Error! Reference source not found.). This expression level isvery similar to that (100 mg) of the WT PmST1 and allows the applicationof the mutant in preparative and large-scale synthesis of SLe^(x)antigens.

X-Ray Crystal Structure of PmST1 M144D Mutant.

The structure of the PmST1 M144D mutant with CMP-3F(axiai)-Neu5Ac wasdetermined to 1.45 Å resolution with R_(factor) and R_(free) values of18.7% and 21.5% respectively Table 3). Error! Reference source notfound. shows the structural comparison between WT PmST1 and M144D mutantwith bound CMP donor. Error! Reference source not found. A shows theoverall structure of WT PmST1 with CMP bound (white tubes), aligned withthe C-terminal domain of the M144D mutant (grey tubes) also with CMPbound (space filled atoms). Error! Reference source not found. B showsthe stereo view of the superposition near the active site. WT PmST1 isshown as white tubes with bound CMP-3F(a)-Neu5Ac (sticks with whitecarbon bonds) and lactose acceptor (sticks with dark grey carbon bonds).The M144D mutant in shown as grey tubes with CMP bound (sticks withlight grey carbon bonds). Error! Reference source not found. C shows theactive site of the ternary crystal structure of PmST1 (PDB 1D: 21HZ)with bound CMP-3F(axial)-Neu5Ac and lactose. The mutation site M144 isunderlined.

The structure resides in the open conformation similar to the wild-typestructure with no substrate (rmsd of 0.50 Å for 385 equivalentα-carbons). However, the M144D structure contains well-ordered electrondensity in the active site that clearly defines the CMP nucleotide. Thesialic acid moiety is disordered, likely due to dynamics and/or multipleconformations in the open state of the enzyme. In the M144D structure,the CMP moiety does not bind as deeply into the pocket of the activesite as the WT PmST1. The base and ribose are situated about 1.5 and 2.0Å respectively, farther out of the active site compared to the WT PmST1.In the wild-type structure, Glu338 forms bidentate hydrogen bondinteractions with both the 2′ and 3′ OH of the CMP ribose. In the M144Dstructure, an ordered water molecule mediates the interaction betweenthe ribose and Glu338. The more shallow binding of the donor nucleotidein the M144D structure does not pull down the β-strand and the ensuingloop that contains Trp270. In comparison, in the wild-type enzyme,donor-nucleotide binding pulls down a β-strand causing Trp270 to pop outof the C-terminal domain, where it helps define the acceptor bindingsite in the sialyltransferase reaction.

PmST1 M144D mutant is more efficient than M144H mutant in sialylatingLe^(x). Overall, the M144D mutation decreased the undesired CMP-Neu5Achydrolysis activity significantly (20-fold) without appreciably changingthe efficiency of the α2-3-sialyltransferase activity when Le^(x) wasused as an acceptor. As a result, M144D showed an overall improvedactivity in sialylation of Le^(x) for the formation of sialyl Le^(x)(SLe^(x)) structures. In comparison, M144H mutant which has a 3.3-folddecreased CMP-Neu5Ac hydrolysis activity and 2.6-fold increasedα2-3-sialyltransferase activity using Le^(x) as an acceptor was lesseffective for directly sialylating Le^(x).

Synthesis of SLe^(x) containing diverse sialic acid forms using PmST1M144D mutant. The application of the PmST1 M144D mutant obtained byprotein structure-based rational design in the synthesis of SLe^(x)containing diverse naturally occurring and non-natural sialic acid formswas demonstrated using an efficient one-pot three-enzyme chemoenzymaticsynthetic system (Error! Reference source not found.). The systemcontained PmST1 M144D mutant, an Neisseria meningitidis CMP-sialic acidsynthetase (NmCSS), and a Pasteurella multocida sialic acid aldolase.N-Acetylmannosamine (ManNAc), mannose, and their derivatives were usedfor in situ synthesis of CMP-sialic acids and derivatives. Le^(x)trisaccharide used as the sialyltransferase acceptor was synthesizedusing a one-pot two-enzyme system containing a bifunctionalL-fucokinase/GDP-fucose pyrophosphorylase (FKP) cloned from Bacteroidesfragilis and a recombinant Helicobacter pylori α1-3-fucosyltransferaseas shown previously. As shown in Error! Reference source not found,SLe^(x) tetrasaccharides containing natural sialic acid forms includingN-acetylneuraminc acid (Neu5Ac), N-glycolylneuraminic acid (Neu5Gc),2-keto-3-deoxy-D-glycero-D-galacto-nonulosonic acid (Kdn), as well as9-O-acetylated Neu5Ac and Neu5Gc were obtained in excellent (85-93%) togood yields (62-64%). The relatively lower yields for the synthesis ofSLe^(x) containing the 9-O-acetyl sialic acid forms were due to thede-O-acetylation process leading to the formation of non-O-acetylatedSLe^(x) oligosaccharides. In addition, SLe^(x) containing non-naturalsialic acid forms including those with an N-azidoacetyl group or anazido group at C-5 or a C-9 azido group were also successfully obtainedin excellent yields (84-91%).

Although the foregoing invention has been described in some detail byway of illustration and example for purposes of clarity ofunderstanding, one of skill in the art will appreciate that certainchanges and modifications may be practiced within the scope of theappended claims. In addition, each reference provided herein isincorporated by reference in its entirety to the same extent as if eachreference was individually incorporated by reference. Where a conflictexists between the instant application and a reference provided herein,the instant application shall dominate.

What is claimed is:
 1. An isolated glycosyltransferase, wherein theamino acid corresponding to position 120 of SEQ ID NO:1 is any aminoacid other than M, the amino acid corresponding to position 247 of SEQID NO:1 is any amino acid other than E, or the amino acid correspondingto position 289 of SEQ ID NO:1 is any amino acid other than R, whereinthe glycosyltransferase has decreased α2-3 sialidase or donor substratehydrolysis activity compared to a control glycosyltransferase, whereinthe amino acid of the glycosyltransferase corresponding to position 120of SEQ ID NO:1 is M, the amino acid corresponding to position 247 of SEQID NO:1 is E, and the amino acid corresponding to position 289 of SEQ IDNO:1 is R, and wherein the glycosyltransferase is a member of theglycosyltransferase family 80 (GT80).
 2. The isolatedglycosyltransferase of claim 1, wherein the isolated glycosyltransferasehas decreased α2-3 sialidase activity, and the amino acid of theglycosyltransferase corresponding to position 247 of SEQ ID NO:1 is anyamino acid other than E, or the amino acid of the glycosyltransferasecorresponding to position 289 of SEQ ID NO:1 is any amino acid otherthan R.
 3. The isolated glycosyltransferase of any of claims 1-2,wherein the ratio of α2-3 sialidase activity for the controlglycosyltransferase to the α2-3 sialidase activity of the isolatedglycosyltransferase is at least 5:1.
 4. The isolated glycosyltransferaseof claim 3, wherein the ratio is at least 10:1.
 5. The isolatedglycosyltransferase of claim 3, wherein the ratio is at least 100:1. 6.The isolated glycosyltransferase of claim 3, wherein the ratio is atleast 1000:1.
 7. The isolated glycosyltransferase of any of claims 1-6,wherein the isolated glycosyltransferase comprises: the amino acidcorresponding to position 247 of SEQ ID NO:1 is any amino acid otherthan E, and the amino acid corresponding to position 289 of SEQ ID NO:1is any amino acid other than R.
 8. The isolated glycosyltransferase ofany of claims 1-7, wherein the isolated glycosyltransferase hasdecreased donor substrate hydrolysis activity, and wherein the aminoacid corresponding to position 120 of SEQ ID NO:1 is any amino acidother than M.
 9. The isolated glycosyltransferase of claim 8, whereinthe ratio of donor substrate hydrolysis activity for the control α2-3sialidase to the donor substrate hydrolysis activity of the isolatedglycosyltransferase is at least 2:1.
 10. The isolatedglycosyltransferase of any of claims 1-9, wherein the amino acidcorresponding to position 120 of SEQ ID NO:1 is any amino acid selectedfrom the group consisting of V, I, L, F, W, P, S, T, A, G, C, Y, N, Q,D, E, K, R, and H.
 11. The isolated glycosyltransferase of any of claims1-10, wherein the amino acid corresponding to position 247 of SEQ IDNO:1 is any amino acid selected from the group consisting of V, I, L, M,F, W, P, S, T, A, G, C, Y, N, Q, D, K, R, and H.
 12. The isolatedglycosyltransferase of any of claims 1-11, wherein the amino acidcorresponding to position 289 of SEQ ID NO:1 is any amino acid selectedfrom the group consisting of V, I, L, M, F, W, P, S, T, A, G, C, Y, N,Q, D, E, K, and H.
 13. The isolated glycosyltransferase of any of claims1-12, wherein the amino acid corresponding to position 120 of SEQ IDNO:1 is D, E, H, K or R, the amino acid corresponding to position 247 ofSEQ ID NO:1 is F, Y or W, or the amino acid corresponding to position289 of SEQ ID NO:1 is Y, F or W.
 14. The isolated glycosyltransferase ofany of claims 1-13, wherein the amino acid corresponding to position 120of SEQ ID NO:1 is D or H, the amino acid corresponding to position 247of SEQ ID NO:1 is F, or the amino acid corresponding to position 289 ofSEQ ID NO:1 is Y.
 15. The isolated glycosyltransferase of any of claims1-14, wherein the glycosyltransferase is an α2-3 sialyltransferase. 16.The isolated glycosyltransferase of claim 15, comprising a motif in thesialyltransferase domain comprising at least one member selected fromthe group consisting of sialyltransferase motif A (YDDGS) andsialyltransferase motif B (KGH).
 17. The isolated glycosyltransferase ofany of claims 1-16, wherein the control glycosyltransferase is SEQ IDNO:1.
 18. The isolated glycosyltransferase of claim 17, wherein theglycosyltransferase comprises a polypeptide sequence having at least 80%sequence identity to SEQ ID NO:1.
 19. The isolated glycosyltransferaseof claim 1, wherein the isolated glycosyltransferase comprises apolypeptide sequence selected from the group consisting of SEQ ID NO: 3(M120D), SEQ ID NO: 5 (M120H), SEQ ID NO: 7 (E247F), SEQ ID NO: 9(R289Y) and SEQ ID NO: 11 (E247F/R289Y).
 20. A recombinant nucleic acidencoding an isolated glycosyltransferase of any of claims 1-19.
 21. Acell comprising an recombinant nucleic acid of claim
 20. 22. The cell ofclaim 21, wherein the cell is selected from the group consisting ofbacteria, yeast, insect, mammalian and plant cells.
 23. A method ofpreparing an oligosaccharide, the method comprising: a) forming areaction mixture comprising an acceptor sugar, a donor substratecomprising a sugar moiety and a nucleotide, and the glycosyltransferaseof any of claims 1-19, under conditions sufficient to transfer the sugarmoiety from the donor substrate to the acceptor sugar, thereby formingthe oligosaccharide.
 24. The method of claim 23, wherein theglycosyltransferase comprises a polypeptide sequence selected from thegroup consisting of SEQ ID NO: 3 (M120D), SEQ ID NO: 5 (M120H), SEQ IDNO: 7 (E247F), SEQ ID NO: 9 (R289Y) and SEQ ID NO: 11 (E247F/R289Y). 25.The method of claim 23, wherein the glycosyltransferase comprises apolypeptide sequence selected from the group consisting of SEQ ID NO: 3(M120D) and SEQ ID NO: 5 (M120H).
 26. The method of claim 23, whereinthe isolated glycosyltransferase comprises a polypeptide sequenceselected from the group consisting of SEQ ID NO: 7 (E247F), SEQ ID NO: 9(R289Y) and SEQ ID NO: 11 (E247F/R289Y).
 27. The method of claim 23,wherein the donor substrate comprises a cytidine5′-monophosphate(CMP)-sialic acid.
 28. The method of claim 27, whereinthe CMP-sialic acid comprises cytidine 5′-monophosphateN-acetylneuraminic acid (CMP-Neu5Ac) or a CMP-Neu5Ac analog.
 29. Themethod of claim 28, further comprising: b) forming a reaction mixturecomprising a CMP-sialic acid synthetase, cytidine triphosphate, andN-acetylneuraminic acid (Neu5Ac) or a Neu5Ac analog, under conditionssuitable to form the CMP-Neu5Ac or CMP-Neu5Ac analog.
 30. The method ofclaim 29, wherein steps a) and b) are performed in one pot.
 31. Themethod of claim 29, further comprising: c) forming a reaction mixturecomprising a sialic acid aldolase, pyruvic acid or derivatives thereof,and N-acetylmannosamine or derivatives thereof, under conditionssuitable to form the Neu5Ac or Neu5Ac analog.
 32. The method of claim31, wherein steps a), b), and c) are performed in one pot.
 33. Themethod of any of claims 23-32, wherein the oligosaccharide is anci2-3-linked sialyloligosaccharide.
 34. The method of claim 23, whereinthe oligosaccharide is a fucosylated oligosaccharide.